Starting phenix.real_space_refine on Mon May 12 21:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/05_2025/9c0f_45082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/05_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_45082/05_2025/9c0f_45082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/05_2025/9c0f_45082.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/05_2025/9c0f_45082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/05_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-5687/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: 5.74, 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: 2.56 Conformation dependent library (CDL) restraints added in 957.3 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: 3.40 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: 3.09 Time building geometry restraints manager: 2.95 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: 0.730 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.720 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- 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 : 1.105 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: 0.2890 time to fit residues: 48.5038 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 : 1.015 ------------------------------------------------------------------------------- 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 = 0.063226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049835 restraints weight = 52933.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051628 restraints weight = 27839.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.052818 restraints weight = 18391.138| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 1.136 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: 0.8050 (mp) cc_final: 0.7572 (mm) REVERT: D 231 HIS cc_start: 0.5702 (m170) cc_final: 0.5457 (m170) REVERT: D 382 MET cc_start: 0.9622 (mmm) cc_final: 0.9138 (tpp) REVERT: D 513 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8586 (mpp) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.2569 time to fit residues: 25.8954 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 : 0.988 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.064076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050598 restraints weight = 53410.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.052387 restraints weight = 28771.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.053625 restraints weight = 19147.717| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9880 Z= 0.145 Angle : 0.652 9.363 13597 Z= 0.357 Chirality : 0.041 0.166 1455 Planarity : 0.004 0.033 1470 Dihedral : 21.764 167.635 1841 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 1.01 % Allowed : 7.84 % Favored : 91.15 % 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: -0.02 (0.26), residues: 956 helix: 0.91 (0.29), residues: 332 sheet: 0.68 (0.54), residues: 83 loop : -0.70 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 138 HIS 0.005 0.001 HIS C 231 PHE 0.014 0.002 PHE C 445 TYR 0.027 0.002 TYR C 312 ARG 0.006 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 362) hydrogen bonds : angle 4.42344 ( 915) metal coordination : bond 0.00487 ( 15) metal coordination : angle 3.05272 ( 6) covalent geometry : bond 0.00313 ( 9865) covalent geometry : angle 0.64870 (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 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.7955 (mp) cc_final: 0.7528 (mm) REVERT: C 496 MET cc_start: 0.7901 (ttp) cc_final: 0.7657 (ttp) REVERT: C 511 MET cc_start: 0.8829 (mmm) cc_final: 0.8517 (mmm) REVERT: C 513 MET cc_start: 0.8249 (mpp) cc_final: 0.8007 (mmm) REVERT: D 382 MET cc_start: 0.9679 (mmm) cc_final: 0.9154 (mmm) REVERT: D 496 MET cc_start: 0.7718 (tmm) cc_final: 0.6981 (tmm) REVERT: D 549 MET cc_start: 0.8562 (ttp) cc_final: 0.7602 (tmm) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.2462 time to fit residues: 22.9433 Evaluate side-chains 58 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 18 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.062047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.048675 restraints weight = 54145.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050317 restraints weight = 30351.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.051432 restraints weight = 20799.224| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9880 Z= 0.189 Angle : 0.638 9.223 13597 Z= 0.349 Chirality : 0.041 0.154 1455 Planarity : 0.004 0.032 1470 Dihedral : 21.632 165.937 1841 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.13 % Allowed : 8.17 % Favored : 89.70 % 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: 0.06 (0.27), residues: 956 helix: 1.21 (0.30), residues: 330 sheet: 0.51 (0.53), residues: 83 loop : -0.78 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 138 HIS 0.005 0.001 HIS C 231 PHE 0.019 0.002 PHE D 129 TYR 0.021 0.002 TYR C 422 ARG 0.005 0.000 ARG D 120 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 362) hydrogen bonds : angle 4.44798 ( 915) metal coordination : bond 0.00937 ( 15) metal coordination : angle 3.20225 ( 6) covalent geometry : bond 0.00419 ( 9865) covalent geometry : angle 0.63428 (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: 19 poor density : 56 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.7970 (mp) cc_final: 0.7573 (mm) REVERT: C 511 MET cc_start: 0.8895 (mmm) cc_final: 0.8618 (mmm) REVERT: C 513 MET cc_start: 0.8677 (mpp) cc_final: 0.8354 (mmt) REVERT: D 183 MET cc_start: 0.8198 (mtt) cc_final: 0.7851 (mtt) REVERT: D 382 MET cc_start: 0.9671 (mmm) cc_final: 0.9011 (mmm) REVERT: D 496 MET cc_start: 0.7682 (tmm) cc_final: 0.7181 (tmm) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.2217 time to fit residues: 21.5311 Evaluate side-chains 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 513 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: 9.9990 chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.060771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.047411 restraints weight = 54413.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.049031 restraints weight = 30623.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.050110 restraints weight = 21104.909| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9880 Z= 0.204 Angle : 0.641 10.398 13597 Z= 0.348 Chirality : 0.042 0.161 1455 Planarity : 0.004 0.038 1470 Dihedral : 21.527 164.107 1841 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 2.02 % Allowed : 8.96 % Favored : 89.03 % 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: -0.19 (0.27), residues: 956 helix: 1.07 (0.29), residues: 343 sheet: 0.04 (0.54), residues: 88 loop : -0.99 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 138 HIS 0.006 0.001 HIS C 408 PHE 0.019 0.002 PHE C 220 TYR 0.023 0.002 TYR C 422 ARG 0.007 0.000 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 362) hydrogen bonds : angle 4.50210 ( 915) metal coordination : bond 0.01302 ( 15) metal coordination : angle 3.75587 ( 6) covalent geometry : bond 0.00454 ( 9865) covalent geometry : angle 0.63629 (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 76 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 LEU cc_start: 0.9013 (tt) cc_final: 0.8506 (tp) REVERT: C 513 MET cc_start: 0.8851 (mpp) cc_final: 0.8427 (mmt) REVERT: D 183 MET cc_start: 0.8352 (mtt) cc_final: 0.8097 (mtt) REVERT: D 308 MET cc_start: 0.8372 (ptm) cc_final: 0.7437 (ptp) REVERT: D 382 MET cc_start: 0.9632 (mmm) cc_final: 0.9031 (mmm) REVERT: D 386 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: D 549 MET cc_start: 0.8624 (ttp) cc_final: 0.7517 (tmm) outliers start: 18 outliers final: 13 residues processed: 67 average time/residue: 0.2327 time to fit residues: 22.2517 Evaluate side-chains 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 373 LEU 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 Chi-restraints excluded: chain D residue 513 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: 0.8980 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 72 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.062408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.048975 restraints weight = 54137.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050658 restraints weight = 29935.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.051798 restraints weight = 20383.512| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4652 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 : 0.594 11.895 13597 Z= 0.317 Chirality : 0.039 0.137 1455 Planarity : 0.003 0.037 1470 Dihedral : 21.424 163.134 1841 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 1.34 % Allowed : 10.41 % Favored : 88.24 % 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: 1.34 (0.30), residues: 343 sheet: 0.47 (0.63), residues: 68 loop : -0.93 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 138 HIS 0.004 0.001 HIS C 231 PHE 0.009 0.001 PHE C 445 TYR 0.019 0.001 TYR C 422 ARG 0.015 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 362) hydrogen bonds : angle 4.05102 ( 915) metal coordination : bond 0.00409 ( 15) metal coordination : angle 2.08847 ( 6) covalent geometry : bond 0.00271 ( 9865) covalent geometry : angle 0.59203 (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 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.8411 (ttp) cc_final: 0.7556 (tpp) REVERT: C 513 MET cc_start: 0.8891 (mpp) cc_final: 0.8685 (mmt) REVERT: D 130 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (ptpp) REVERT: D 183 MET cc_start: 0.8267 (mtt) cc_final: 0.7973 (mtt) REVERT: D 308 MET cc_start: 0.8242 (ptm) cc_final: 0.7346 (ptp) REVERT: D 382 MET cc_start: 0.9676 (mmm) cc_final: 0.9064 (mmm) REVERT: D 409 MET cc_start: 0.7946 (tpp) cc_final: 0.7722 (mmp) REVERT: D 549 MET cc_start: 0.8525 (ttp) cc_final: 0.7508 (tmm) outliers start: 12 outliers final: 6 residues processed: 66 average time/residue: 0.2495 time to fit residues: 23.1193 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 : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 130 LYS 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: 0.0270 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 40.0000 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.7242 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.062244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.048709 restraints weight = 54502.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.050404 restraints weight = 30063.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.051548 restraints weight = 20470.545| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4801 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= 0.124 Angle : 0.573 11.581 13597 Z= 0.308 Chirality : 0.039 0.140 1455 Planarity : 0.003 0.032 1470 Dihedral : 21.400 160.545 1841 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.46 % Allowed : 9.97 % Favored : 88.58 % 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: 0.23 (0.28), residues: 956 helix: 1.60 (0.30), residues: 337 sheet: 1.13 (0.66), residues: 60 loop : -0.91 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 138 HIS 0.004 0.001 HIS C 231 PHE 0.009 0.001 PHE C 445 TYR 0.021 0.001 TYR C 422 ARG 0.002 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 362) hydrogen bonds : angle 3.94078 ( 915) metal coordination : bond 0.00491 ( 15) metal coordination : angle 2.08532 ( 6) covalent geometry : bond 0.00273 ( 9865) covalent geometry : angle 0.57153 (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: 13 poor density : 58 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.8369 (ttp) cc_final: 0.7572 (tpp) REVERT: C 513 MET cc_start: 0.9034 (mpp) cc_final: 0.8680 (mmt) REVERT: D 183 MET cc_start: 0.8257 (mtt) cc_final: 0.7944 (mtt) REVERT: D 292 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8002 (pt) REVERT: D 382 MET cc_start: 0.9677 (mmm) cc_final: 0.9044 (mmm) REVERT: D 409 MET cc_start: 0.7832 (tpp) cc_final: 0.7613 (mmp) REVERT: D 549 MET cc_start: 0.8539 (ttp) cc_final: 0.7500 (tmm) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 0.2177 time to fit residues: 21.0220 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 : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 373 LEU 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: 1.9990 chunk 42 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 ASN ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** 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 = 0.3769 r_free = 0.3769 target = 0.061231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.047802 restraints weight = 54953.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.049465 restraints weight = 30612.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.050558 restraints weight = 20931.201| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4933 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= 0.162 Angle : 0.600 11.212 13597 Z= 0.325 Chirality : 0.040 0.180 1455 Planarity : 0.003 0.033 1470 Dihedral : 21.397 158.354 1841 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.23 % Allowed : 10.19 % 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: 0.13 (0.28), residues: 956 helix: 1.44 (0.30), residues: 342 sheet: 0.79 (0.65), residues: 70 loop : -0.93 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 138 HIS 0.004 0.001 HIS C 231 PHE 0.013 0.001 PHE C 149 TYR 0.020 0.002 TYR C 422 ARG 0.002 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 362) hydrogen bonds : angle 4.15323 ( 915) metal coordination : bond 0.00972 ( 15) metal coordination : angle 2.60271 ( 6) covalent geometry : bond 0.00360 ( 9865) covalent geometry : angle 0.59785 (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 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.8412 (ttp) cc_final: 0.7587 (tpp) REVERT: C 513 MET cc_start: 0.8977 (mpp) cc_final: 0.8499 (mmt) REVERT: D 156 MET cc_start: 0.8842 (ttm) cc_final: 0.8477 (mmm) REVERT: D 183 MET cc_start: 0.8313 (mtt) cc_final: 0.8073 (mtt) REVERT: D 292 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8076 (pt) REVERT: D 382 MET cc_start: 0.9666 (mmm) cc_final: 0.9030 (mmm) REVERT: D 409 MET cc_start: 0.7978 (tpp) cc_final: 0.7769 (mmp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.2363 time to fit residues: 22.0612 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.062583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049265 restraints weight = 54288.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.050971 restraints weight = 30145.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.052109 restraints weight = 20479.334| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9880 Z= 0.116 Angle : 0.592 12.299 13597 Z= 0.312 Chirality : 0.039 0.173 1455 Planarity : 0.003 0.064 1470 Dihedral : 21.304 158.585 1841 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 1.23 % Allowed : 10.30 % 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: 0.19 (0.28), residues: 956 helix: 1.44 (0.30), residues: 344 sheet: 1.27 (0.69), residues: 60 loop : -0.89 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 138 HIS 0.004 0.001 HIS C 231 PHE 0.009 0.001 PHE C 326 TYR 0.017 0.001 TYR C 312 ARG 0.023 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 362) hydrogen bonds : angle 3.91571 ( 915) metal coordination : bond 0.00312 ( 15) metal coordination : angle 1.81678 ( 6) covalent geometry : bond 0.00255 ( 9865) covalent geometry : angle 0.59131 (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: 11 poor density : 61 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9191 (mttt) cc_final: 0.8883 (mtpt) REVERT: C 278 MET cc_start: 0.8350 (ttp) cc_final: 0.7606 (tpp) REVERT: C 511 MET cc_start: 0.9254 (mmm) cc_final: 0.9035 (mmm) REVERT: C 513 MET cc_start: 0.8781 (mpp) cc_final: 0.8544 (mmt) REVERT: D 156 MET cc_start: 0.8771 (ttm) cc_final: 0.8482 (mmm) REVERT: D 183 MET cc_start: 0.8227 (mtt) cc_final: 0.7973 (mtt) REVERT: D 382 MET cc_start: 0.9679 (mmm) cc_final: 0.9062 (mmm) REVERT: D 459 MET cc_start: 0.8226 (ptp) cc_final: 0.8021 (ptm) REVERT: D 549 MET cc_start: 0.8543 (ttp) cc_final: 0.7500 (tmm) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.2531 time to fit residues: 24.2915 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 26 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 417 GLN ** C 519 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.061220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047859 restraints weight = 54950.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.049509 restraints weight = 30450.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.050580 restraints weight = 20725.853| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9880 Z= 0.174 Angle : 0.627 12.040 13597 Z= 0.334 Chirality : 0.040 0.144 1455 Planarity : 0.003 0.033 1470 Dihedral : 21.330 156.694 1841 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.08 % 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 : 0.00 % 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: 0.13 (0.28), residues: 956 helix: 1.42 (0.30), residues: 342 sheet: 0.97 (0.66), residues: 70 loop : -0.95 (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 0.013 0.001 PHE C 149 TYR 0.030 0.002 TYR C 422 ARG 0.003 0.000 ARG D 265 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 362) hydrogen bonds : angle 4.19055 ( 915) metal coordination : bond 0.01101 ( 15) metal coordination : angle 2.49024 ( 6) covalent geometry : bond 0.00388 ( 9865) covalent geometry : angle 0.62489 (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 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 VAL cc_start: 0.7815 (t) cc_final: 0.7609 (m) REVERT: C 278 MET cc_start: 0.8435 (ttp) cc_final: 0.7606 (tpp) REVERT: C 308 MET cc_start: 0.7846 (mtp) cc_final: 0.7196 (ttp) REVERT: C 513 MET cc_start: 0.8953 (mpp) cc_final: 0.8491 (mmt) REVERT: D 156 MET cc_start: 0.8825 (ttm) cc_final: 0.8494 (mmm) REVERT: D 183 MET cc_start: 0.8371 (mtt) cc_final: 0.8151 (mtt) REVERT: D 382 MET cc_start: 0.9657 (mmm) cc_final: 0.8997 (mmm) REVERT: D 409 MET cc_start: 0.7675 (mmp) cc_final: 0.7469 (mmp) REVERT: D 549 MET cc_start: 0.8634 (ttp) cc_final: 0.7645 (tmm) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.2509 time to fit residues: 22.3929 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 : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 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 46 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.0170 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 overall best weight: 2.6424 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.061683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.048325 restraints weight = 54315.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.049974 restraints weight = 30197.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.051017 restraints weight = 20568.413| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9880 Z= 0.147 Angle : 0.636 12.551 13597 Z= 0.335 Chirality : 0.040 0.145 1455 Planarity : 0.005 0.143 1470 Dihedral : 21.309 157.094 1841 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.23 % Allowed : 10.86 % Favored : 87.91 % 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: 0.14 (0.28), residues: 956 helix: 1.38 (0.30), residues: 342 sheet: 1.52 (0.70), residues: 60 loop : -0.93 (0.26), residues: 554 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 0.010 0.001 PHE D 249 TYR 0.031 0.002 TYR D 260 ARG 0.019 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 362) hydrogen bonds : angle 4.10477 ( 915) metal coordination : bond 0.00802 ( 15) metal coordination : angle 2.26291 ( 6) covalent geometry : bond 0.00330 ( 9865) covalent geometry : angle 0.63396 (13591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.68 seconds wall clock time: 61 minutes 27.78 seconds (3687.78 seconds total)