Starting phenix.real_space_refine on Wed Apr 30 08:30:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/04_2025/9c0f_45082.cif" } resolution = 3.6 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= 0.001 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 Zn 4 6.06 5 P 70 5.49 5 S 60 5.16 5 C 5845 2.51 5 N 1682 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 725 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3883 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4185 Classifications: {'peptide': 504} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 484} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5131 SG CYS C 550 61.208 48.152 33.030 1.00 65.65 S ATOM 5157 SG CYS C 553 59.580 50.916 32.456 1.00 69.88 S ATOM 4997 SG CYS C 534 52.649 39.523 29.596 1.00 66.98 S ATOM 5021 SG CYS C 537 50.886 37.901 27.221 1.00 71.35 S ATOM 5222 SG CYS C 562 54.572 38.672 26.797 1.00 70.35 S ATOM 9316 SG CYS D 550 72.168 38.504 21.727 1.00104.21 S ATOM 9342 SG CYS D 553 75.805 38.342 20.784 1.00108.94 S ATOM 9206 SG CYS D 537 77.529 32.093 35.072 1.00114.33 S ATOM 9407 SG CYS D 562 74.973 36.015 34.245 1.00105.23 S Time building chain proxies: 5.73, per 1000 atoms: 0.60 Number of scatterers: 9507 At special positions: 0 Unit cell: (108.36, 134.16, 98.9, 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) Zn 4 29.99 S 60 16.00 P 70 15.00 O 1846 8.00 N 1682 7.00 C 5845 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: 2.44 Conformation dependent library (CDL) restraints added in 892.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" NE2 HIS C 567 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 516 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 550 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 553 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" ND1 HIS C 558 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 537 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 534 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 516 " pdb="ZN ZN D 601 " - pdb=" NE2 HIS D 567 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 550 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 553 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 558 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 537 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 562 " Number of angles added : 6 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 39.4% alpha, 11.0% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 107 through 125 Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 163 through 169 removed outlier: 4.063A pdb=" N TYR C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.358A pdb=" N GLY C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.571A pdb=" N ALA C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 227 Proline residue: C 222 - end of helix removed outlier: 3.526A pdb=" N ILE C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.796A pdb=" N LYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.759A pdb=" N LYS C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 430 through 455 Processing helix chain 'C' and resid 460 through 473 Processing helix chain 'C' and resid 505 through 510 removed outlier: 4.345A pdb=" N LEU C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.747A pdb=" N VAL C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.007A pdb=" N LYS C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C 567 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 107 through 125 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.850A pdb=" N LYS D 130 " --> pdb=" O ASN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 156 removed outlier: 3.814A pdb=" N LYS D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.935A pdb=" N GLU D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.641A pdb=" N TYR D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 222 - end of helix removed outlier: 4.395A pdb=" N TYR D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.134A pdb=" N ALA D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 400 through 408 Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.500A pdb=" N GLN D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 418' Processing helix chain 'D' and resid 419 through 426 removed outlier: 3.801A pdb=" N SER D 423 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE D 424 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 455 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.815A pdb=" N HIS D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 569 Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AA2, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.610A pdb=" N LEU C 267 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET C 278 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG C 265 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE C 280 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 263 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 382 through 386 Processing sheet with id=AA4, first strand: chain 'C' and resid 518 through 520 removed outlier: 4.151A pdb=" N TYR C 548 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE C 555 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 532 through 533 Processing sheet with id=AA6, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.707A pdb=" N LEU D 267 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET D 278 " --> pdb=" O ARG D 265 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG D 265 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU D 234 " --> pdb=" O TYR D 307 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR D 331 " --> pdb=" O MET D 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AA8, first strand: chain 'D' and resid 518 through 520 Processing sheet with id=AA9, first strand: chain 'D' and resid 532 through 533 278 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1514 1.30 - 1.44: 3413 1.44 - 1.58: 4693 1.58 - 1.72: 158 1.72 - 1.86: 87 Bond restraints: 9865 Sorted by residual: bond pdb=" CB HIS D 471 " pdb=" CG HIS D 471 " ideal model delta sigma weight residual 1.497 1.345 0.152 1.40e-02 5.10e+03 1.18e+02 bond pdb=" CB HIS C 231 " pdb=" CG HIS C 231 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.20e+01 bond pdb=" CB PHE D 464 " pdb=" CG PHE D 464 " ideal model delta sigma weight residual 1.502 1.304 0.198 2.30e-02 1.89e+03 7.43e+01 bond pdb=" CB HIS D 558 " pdb=" CG HIS D 558 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.58e+01 bond pdb=" CB PHE C 464 " pdb=" CG PHE C 464 " ideal model delta sigma weight residual 1.502 1.323 0.179 2.30e-02 1.89e+03 6.05e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11558 2.52 - 5.03: 1730 5.03 - 7.55: 255 7.55 - 10.06: 39 10.06 - 12.58: 9 Bond angle restraints: 13591 Sorted by residual: angle pdb=" N VAL D 241 " pdb=" CA VAL D 241 " pdb=" C VAL D 241 " ideal model delta sigma weight residual 109.02 117.60 -8.58 9.30e-01 1.16e+00 8.52e+01 angle pdb=" C LYS D 229 " pdb=" N PRO D 230 " pdb=" CA PRO D 230 " ideal model delta sigma weight residual 120.52 129.30 -8.78 9.90e-01 1.02e+00 7.86e+01 angle pdb=" C THR C 176 " pdb=" N PRO C 177 " pdb=" CA PRO C 177 " ideal model delta sigma weight residual 119.56 128.60 -9.04 1.02e+00 9.61e-01 7.86e+01 angle pdb=" C THR D 176 " pdb=" N PRO D 177 " pdb=" CA PRO D 177 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 angle pdb=" N ILE C 240 " pdb=" CA ILE C 240 " pdb=" C ILE C 240 " ideal model delta sigma weight residual 108.11 119.48 -11.37 1.40e+00 5.10e-01 6.59e+01 ... (remaining 13586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 5400 31.31 - 62.62: 355 62.62 - 93.93: 8 93.93 - 125.24: 0 125.24 - 156.55: 1 Dihedral angle restraints: 5764 sinusoidal: 2892 harmonic: 2872 Sorted by residual: dihedral pdb=" C PHE C 248 " pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" CB PHE C 248 " ideal model delta harmonic sigma weight residual -122.60 -110.79 -11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" C ARG C 547 " pdb=" N ARG C 547 " pdb=" CA ARG C 547 " pdb=" CB ARG C 547 " ideal model delta harmonic sigma weight residual -122.60 -133.87 11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS C 541 " pdb=" N LYS C 541 " pdb=" CA LYS C 541 " pdb=" CB LYS C 541 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 5761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1036 0.114 - 0.228: 350 0.228 - 0.341: 58 0.341 - 0.455: 7 0.455 - 0.569: 4 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA TYR D 260 " pdb=" N TYR D 260 " pdb=" C TYR D 260 " pdb=" CB TYR D 260 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CG LEU C 288 " pdb=" CB LEU C 288 " pdb=" CD1 LEU C 288 " pdb=" CD2 LEU C 288 " both_signs ideal model delta sigma weight residual False -2.59 -3.09 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CA ARG C 547 " pdb=" N ARG C 547 " pdb=" C ARG C 547 " pdb=" CB ARG C 547 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 1452 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA A 18 " 0.170 2.00e-02 2.50e+03 7.04e-02 1.36e+02 pdb=" N9 DA A 18 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DA A 18 " -0.075 2.00e-02 2.50e+03 pdb=" N7 DA A 18 " -0.036 2.00e-02 2.50e+03 pdb=" C5 DA A 18 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DA A 18 " 0.024 2.00e-02 2.50e+03 pdb=" N6 DA A 18 " 0.102 2.00e-02 2.50e+03 pdb=" N1 DA A 18 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA A 18 " -0.035 2.00e-02 2.50e+03 pdb=" N3 DA A 18 " -0.052 2.00e-02 2.50e+03 pdb=" C4 DA A 18 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 17 " 0.123 2.00e-02 2.50e+03 5.23e-02 7.51e+01 pdb=" N9 DA A 17 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA A 17 " -0.049 2.00e-02 2.50e+03 pdb=" N7 DA A 17 " -0.037 2.00e-02 2.50e+03 pdb=" C5 DA A 17 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DA A 17 " 0.025 2.00e-02 2.50e+03 pdb=" N6 DA A 17 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DA A 17 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DA A 17 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DA A 17 " -0.053 2.00e-02 2.50e+03 pdb=" C4 DA A 17 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B -24 " 0.100 2.00e-02 2.50e+03 4.83e-02 6.42e+01 pdb=" N9 DA B -24 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DA B -24 " -0.061 2.00e-02 2.50e+03 pdb=" N7 DA B -24 " -0.044 2.00e-02 2.50e+03 pdb=" C5 DA B -24 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DA B -24 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA B -24 " 0.083 2.00e-02 2.50e+03 pdb=" N1 DA B -24 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DA B -24 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DA B -24 " -0.029 2.00e-02 2.50e+03 pdb=" C4 DA B -24 " -0.011 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2943 2.83 - 3.35: 8450 3.35 - 3.87: 15941 3.87 - 4.38: 19590 4.38 - 4.90: 29074 Nonbonded interactions: 75998 Sorted by model distance: nonbonded pdb=" OG1 THR C 428 " pdb=" N VAL C 429 " model vdw 2.314 3.120 nonbonded pdb=" OG SER C 423 " pdb=" N ILE C 424 " model vdw 2.321 3.120 nonbonded pdb=" OG SER C 367 " pdb=" N LYS C 368 " model vdw 2.322 3.120 nonbonded pdb=" N LEU D 289 " pdb=" O LEU D 289 " model vdw 2.387 2.496 nonbonded pdb=" O5' DG B -34 " pdb=" O4' DG B -34 " model vdw 2.411 2.432 ... (remaining 75993 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 78 through 284 or resid 288 through 332 or resid 341 throu \ gh 476 or resid 495 through 572 or resid 601 through 602)) } 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 group one per residue 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: 0.950 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.350 Find NCS groups from input model: 0.400 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.028 0.454 9880 Z= 1.463 Angle : 1.942 29.708 13597 Z= 1.280 Chirality : 0.114 0.569 1455 Planarity : 0.011 0.085 1470 Dihedral : 16.991 156.551 3908 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.70 % Rotamer: Outliers : 0.34 % Allowed : 0.90 % Favored : 98.77 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.25), residues: 956 helix: -0.91 (0.26), residues: 324 sheet: 0.73 (0.49), residues: 95 loop : -0.05 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.009 TRP C 243 HIS 0.015 0.003 HIS C 378 PHE 0.033 0.008 PHE D 563 TYR 0.085 0.012 TYR D 312 ARG 0.005 0.001 ARG D 533 Details of bonding type rmsd hydrogen bonds : bond 0.22469 ( 362) hydrogen bonds : angle 6.83821 ( 915) metal coordination : bond 0.24310 ( 15) metal coordination : angle 21.34610 ( 6) covalent geometry : bond 0.02627 ( 9865) covalent geometry : angle 1.88991 (13591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7622 (ttt) cc_final: 0.7409 (ttt) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 0.2914 time to fit residues: 48.7969 Evaluate side-chains 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 305 HIS D 317 ASN ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.063269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.049942 restraints weight = 53180.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.051712 restraints weight = 28158.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.052894 restraints weight = 18711.770| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9880 Z= 0.251 Angle : 0.813 11.203 13597 Z= 0.449 Chirality : 0.047 0.386 1455 Planarity : 0.005 0.042 1470 Dihedral : 21.654 157.721 1841 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.38 % Rotamer: Outliers : 1.79 % Allowed : 6.94 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.25), residues: 956 helix: 0.34 (0.28), residues: 333 sheet: 0.83 (0.57), residues: 73 loop : -0.71 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 138 HIS 0.007 0.002 HIS D 73 PHE 0.020 0.002 PHE C 149 TYR 0.041 0.002 TYR C 422 ARG 0.007 0.001 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.07442 ( 362) hydrogen bonds : angle 5.12611 ( 915) metal coordination : bond 0.01060 ( 15) metal coordination : angle 5.86622 ( 6) covalent geometry : bond 0.00548 ( 9865) covalent geometry : angle 0.80409 (13591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.8051 (mp) cc_final: 0.7573 (mm) REVERT: D 231 HIS cc_start: 0.5699 (m170) cc_final: 0.5455 (m170) REVERT: D 382 MET cc_start: 0.9622 (mmm) cc_final: 0.9138 (tpp) REVERT: D 513 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8581 (mpp) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.2621 time to fit residues: 26.3034 Evaluate side-chains 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN C 196 HIS ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.065888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.052950 restraints weight = 57078.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054701 restraints weight = 31454.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.055829 restraints weight = 21255.243| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9880 Z= 0.139 Angle : 0.650 9.292 13597 Z= 0.355 Chirality : 0.041 0.172 1455 Planarity : 0.004 0.033 1470 Dihedral : 21.731 168.324 1841 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 1.01 % Allowed : 7.61 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.01 (0.26), residues: 956 helix: 0.90 (0.29), residues: 331 sheet: 0.76 (0.54), residues: 83 loop : -0.68 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 138 HIS 0.004 0.001 HIS C 231 PHE 0.014 0.001 PHE C 445 TYR 0.026 0.002 TYR C 312 ARG 0.006 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 362) hydrogen bonds : angle 4.38087 ( 915) metal coordination : bond 0.00540 ( 15) metal coordination : angle 2.94203 ( 6) covalent geometry : bond 0.00296 ( 9865) covalent geometry : angle 0.64739 (13591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.7965 (mp) cc_final: 0.7622 (mm) REVERT: C 496 MET cc_start: 0.7910 (ttp) cc_final: 0.7682 (ttp) REVERT: D 382 MET cc_start: 0.9686 (mmm) cc_final: 0.9165 (mmm) REVERT: D 496 MET cc_start: 0.7674 (tmm) cc_final: 0.6931 (tmm) REVERT: D 549 MET cc_start: 0.8606 (ttp) cc_final: 0.7730 (tmm) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.2351 time to fit residues: 22.5372 Evaluate side-chains 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 0.0570 chunk 18 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.061924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.048524 restraints weight = 54299.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050172 restraints weight = 30470.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051289 restraints weight = 20889.457| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9880 Z= 0.201 Angle : 0.653 9.252 13597 Z= 0.356 Chirality : 0.042 0.170 1455 Planarity : 0.004 0.032 1470 Dihedral : 21.629 166.243 1841 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 2.02 % Allowed : 7.50 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.03 (0.27), residues: 956 helix: 1.20 (0.30), residues: 330 sheet: 0.57 (0.53), residues: 83 loop : -0.82 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 138 HIS 0.005 0.001 HIS C 231 PHE 0.018 0.002 PHE C 149 TYR 0.029 0.002 TYR C 422 ARG 0.007 0.000 ARG D 120 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 362) hydrogen bonds : angle 4.47306 ( 915) metal coordination : bond 0.01081 ( 15) metal coordination : angle 3.45326 ( 6) covalent geometry : bond 0.00445 ( 9865) covalent geometry : angle 0.64946 (13591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.7903 (mp) cc_final: 0.7654 (mm) REVERT: C 322 MET cc_start: 0.9066 (mmm) cc_final: 0.8844 (mmm) REVERT: C 513 MET cc_start: 0.8398 (mpp) cc_final: 0.8191 (mmt) REVERT: D 183 MET cc_start: 0.8247 (mtt) cc_final: 0.7941 (mtt) REVERT: D 382 MET cc_start: 0.9638 (mmm) cc_final: 0.9049 (mmm) REVERT: D 496 MET cc_start: 0.7667 (tmm) cc_final: 0.7187 (tmm) outliers start: 18 outliers final: 13 residues processed: 67 average time/residue: 0.2428 time to fit residues: 23.8674 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.060546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.047134 restraints weight = 54195.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.048751 restraints weight = 30550.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.049831 restraints weight = 21078.513| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9880 Z= 0.213 Angle : 0.653 10.621 13597 Z= 0.355 Chirality : 0.042 0.178 1455 Planarity : 0.004 0.044 1470 Dihedral : 21.556 164.413 1841 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.90 % Allowed : 8.62 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.27 (0.27), residues: 956 helix: 1.01 (0.29), residues: 341 sheet: 0.04 (0.54), residues: 88 loop : -1.03 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 138 HIS 0.006 0.001 HIS C 408 PHE 0.021 0.002 PHE C 220 TYR 0.030 0.002 TYR C 422 ARG 0.007 0.001 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 362) hydrogen bonds : angle 4.58244 ( 915) metal coordination : bond 0.01429 ( 15) metal coordination : angle 4.21268 ( 6) covalent geometry : bond 0.00474 ( 9865) covalent geometry : angle 0.64746 (13591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 LEU cc_start: 0.9050 (tt) cc_final: 0.8584 (tp) REVERT: C 322 MET cc_start: 0.9127 (mmm) cc_final: 0.8918 (mmm) REVERT: C 513 MET cc_start: 0.8629 (mpp) cc_final: 0.8238 (mmt) REVERT: D 183 MET cc_start: 0.8409 (mtt) cc_final: 0.8190 (mtt) REVERT: D 308 MET cc_start: 0.8394 (ptm) cc_final: 0.7473 (ptp) REVERT: D 382 MET cc_start: 0.9591 (mmm) cc_final: 0.9014 (mmm) REVERT: D 386 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: D 549 MET cc_start: 0.8616 (ttp) cc_final: 0.7518 (tmm) outliers start: 17 outliers final: 12 residues processed: 67 average time/residue: 0.3122 time to fit residues: 30.6129 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.062375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048951 restraints weight = 54308.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050638 restraints weight = 30056.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.051783 restraints weight = 20441.061| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9880 Z= 0.123 Angle : 0.593 11.470 13597 Z= 0.317 Chirality : 0.039 0.147 1455 Planarity : 0.003 0.037 1470 Dihedral : 21.434 162.980 1841 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.01 % Allowed : 10.53 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.04 (0.27), residues: 956 helix: 1.48 (0.30), residues: 338 sheet: 0.41 (0.63), residues: 68 loop : -0.99 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 138 HIS 0.008 0.001 HIS D 231 PHE 0.009 0.001 PHE D 249 TYR 0.024 0.001 TYR C 422 ARG 0.013 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 362) hydrogen bonds : angle 4.05872 ( 915) metal coordination : bond 0.00454 ( 15) metal coordination : angle 2.24495 ( 6) covalent geometry : bond 0.00267 ( 9865) covalent geometry : angle 0.59126 (13591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9286 (mttt) cc_final: 0.8989 (mtpt) REVERT: C 289 LEU cc_start: 0.9088 (tt) cc_final: 0.8753 (tp) REVERT: C 322 MET cc_start: 0.9231 (mmm) cc_final: 0.9018 (mmm) REVERT: C 437 MET cc_start: 0.7876 (tpt) cc_final: 0.7486 (ttp) REVERT: D 130 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (ptpp) REVERT: D 183 MET cc_start: 0.8271 (mtt) cc_final: 0.7998 (mtt) REVERT: D 292 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8083 (pt) REVERT: D 382 MET cc_start: 0.9628 (mmm) cc_final: 0.9020 (mmm) REVERT: D 409 MET cc_start: 0.7868 (tpp) cc_final: 0.7616 (mmp) REVERT: D 549 MET cc_start: 0.8512 (ttp) cc_final: 0.7472 (tmm) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.2495 time to fit residues: 22.8000 Evaluate side-chains 62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 95 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.061183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.047705 restraints weight = 55017.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049357 restraints weight = 30711.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.050407 restraints weight = 21023.493| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9880 Z= 0.156 Angle : 0.588 9.193 13597 Z= 0.318 Chirality : 0.040 0.139 1455 Planarity : 0.003 0.031 1470 Dihedral : 21.450 159.381 1841 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.57 % Allowed : 9.85 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.27), residues: 956 helix: 1.46 (0.30), residues: 341 sheet: 0.65 (0.63), residues: 70 loop : -0.98 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 138 HIS 0.012 0.001 HIS D 231 PHE 0.013 0.001 PHE C 149 TYR 0.023 0.002 TYR C 422 ARG 0.003 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 362) hydrogen bonds : angle 4.17134 ( 915) metal coordination : bond 0.00853 ( 15) metal coordination : angle 2.76503 ( 6) covalent geometry : bond 0.00345 ( 9865) covalent geometry : angle 0.58476 (13591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 LEU cc_start: 0.9104 (tt) cc_final: 0.8784 (tp) REVERT: C 437 MET cc_start: 0.7898 (tpt) cc_final: 0.7615 (ttp) REVERT: D 130 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (ptpp) REVERT: D 183 MET cc_start: 0.8317 (mtt) cc_final: 0.8087 (mtt) REVERT: D 292 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8134 (pt) REVERT: D 382 MET cc_start: 0.9668 (mmm) cc_final: 0.9058 (mmm) REVERT: D 409 MET cc_start: 0.8011 (tpp) cc_final: 0.7804 (mmp) outliers start: 14 outliers final: 5 residues processed: 67 average time/residue: 0.2373 time to fit residues: 22.4289 Evaluate side-chains 63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.060835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047462 restraints weight = 55892.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.049085 restraints weight = 31247.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.050160 restraints weight = 21442.369| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9880 Z= 0.174 Angle : 0.604 8.851 13597 Z= 0.326 Chirality : 0.040 0.142 1455 Planarity : 0.004 0.051 1470 Dihedral : 21.444 157.546 1841 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.57 % Allowed : 10.08 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.28), residues: 956 helix: 1.45 (0.30), residues: 341 sheet: 0.61 (0.65), residues: 70 loop : -1.04 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 138 HIS 0.010 0.001 HIS D 231 PHE 0.013 0.001 PHE C 149 TYR 0.021 0.002 TYR C 422 ARG 0.017 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 362) hydrogen bonds : angle 4.19219 ( 915) metal coordination : bond 0.01040 ( 15) metal coordination : angle 3.00774 ( 6) covalent geometry : bond 0.00388 ( 9865) covalent geometry : angle 0.60117 (13591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9222 (mttt) cc_final: 0.8932 (mtpt) REVERT: C 278 MET cc_start: 0.8422 (ttp) cc_final: 0.7751 (tpt) REVERT: C 437 MET cc_start: 0.7895 (tpt) cc_final: 0.7579 (ttp) REVERT: D 130 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (ptpp) REVERT: D 183 MET cc_start: 0.8353 (mtt) cc_final: 0.8110 (mtt) REVERT: D 287 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8731 (tpt170) REVERT: D 292 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8199 (pt) REVERT: D 382 MET cc_start: 0.9659 (mmm) cc_final: 0.9044 (mmm) REVERT: D 549 MET cc_start: 0.8593 (ttp) cc_final: 0.7624 (tmm) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.2492 time to fit residues: 23.7628 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.061772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.048453 restraints weight = 54343.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050112 restraints weight = 30370.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.051229 restraints weight = 20739.237| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9880 Z= 0.127 Angle : 0.577 9.051 13597 Z= 0.309 Chirality : 0.039 0.146 1455 Planarity : 0.003 0.032 1470 Dihedral : 21.368 157.173 1841 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.57 % Allowed : 10.30 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.28), residues: 956 helix: 1.53 (0.30), residues: 341 sheet: 0.59 (0.64), residues: 70 loop : -0.97 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 138 HIS 0.007 0.001 HIS D 231 PHE 0.009 0.001 PHE D 249 TYR 0.019 0.001 TYR C 422 ARG 0.002 0.000 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 362) hydrogen bonds : angle 3.99883 ( 915) metal coordination : bond 0.00589 ( 15) metal coordination : angle 2.26851 ( 6) covalent geometry : bond 0.00280 ( 9865) covalent geometry : angle 0.57552 (13591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9221 (mttt) cc_final: 0.8912 (mtpt) REVERT: C 437 MET cc_start: 0.7900 (tpt) cc_final: 0.7558 (ttp) REVERT: D 183 MET cc_start: 0.8255 (mtt) cc_final: 0.7997 (mtt) REVERT: D 382 MET cc_start: 0.9672 (mmm) cc_final: 0.9052 (mmm) REVERT: D 549 MET cc_start: 0.8556 (ttp) cc_final: 0.7574 (tmm) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.2509 time to fit residues: 24.1545 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.063248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.049871 restraints weight = 55234.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051558 restraints weight = 30762.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.052702 restraints weight = 20943.162| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9880 Z= 0.114 Angle : 0.593 10.016 13597 Z= 0.312 Chirality : 0.039 0.148 1455 Planarity : 0.004 0.056 1470 Dihedral : 21.258 157.813 1841 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.01 % Allowed : 10.86 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.28), residues: 956 helix: 1.48 (0.31), residues: 342 sheet: 0.82 (0.64), residues: 70 loop : -0.85 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 138 HIS 0.008 0.001 HIS D 231 PHE 0.009 0.001 PHE C 326 TYR 0.018 0.001 TYR C 422 ARG 0.015 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 362) hydrogen bonds : angle 3.86336 ( 915) metal coordination : bond 0.00513 ( 15) metal coordination : angle 1.64224 ( 6) covalent geometry : bond 0.00244 ( 9865) covalent geometry : angle 0.59214 (13591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9213 (mttt) cc_final: 0.8908 (mtpt) REVERT: C 278 MET cc_start: 0.8317 (ttp) cc_final: 0.7511 (tpp) REVERT: C 308 MET cc_start: 0.7736 (mtp) cc_final: 0.7243 (ttp) REVERT: C 356 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6831 (mtt180) REVERT: C 437 MET cc_start: 0.7808 (tpt) cc_final: 0.7477 (ttp) REVERT: D 183 MET cc_start: 0.8067 (mtt) cc_final: 0.7839 (mtt) REVERT: D 382 MET cc_start: 0.9691 (mmm) cc_final: 0.9063 (mmm) REVERT: D 409 MET cc_start: 0.7298 (mmp) cc_final: 0.7021 (mmp) REVERT: D 549 MET cc_start: 0.8494 (ttp) cc_final: 0.7513 (tmm) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.2673 time to fit residues: 24.1655 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.062690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.049624 restraints weight = 57657.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.051297 restraints weight = 32393.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.052409 restraints weight = 22032.131| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9880 Z= 0.138 Angle : 0.597 11.384 13597 Z= 0.315 Chirality : 0.039 0.146 1455 Planarity : 0.003 0.035 1470 Dihedral : 21.253 157.051 1841 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 1.12 % Allowed : 10.41 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.28), residues: 956 helix: 1.51 (0.31), residues: 342 sheet: 0.77 (0.65), residues: 70 loop : -0.88 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 138 HIS 0.004 0.001 HIS C 231 PHE 0.011 0.001 PHE C 461 TYR 0.026 0.001 TYR C 422 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 362) hydrogen bonds : angle 3.94454 ( 915) metal coordination : bond 0.00689 ( 15) metal coordination : angle 2.07911 ( 6) covalent geometry : bond 0.00307 ( 9865) covalent geometry : angle 0.59518 (13591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.03 seconds wall clock time: 64 minutes 0.81 seconds (3840.81 seconds total)