Starting phenix.real_space_refine on Sun Aug 24 08:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2d_18839/08_2025/8r2d_18839.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 127 5.16 5 C 11676 2.51 5 N 3094 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5468 Classifications: {'peptide': 718} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3786 Classifications: {'peptide': 483} Link IDs: {'PCIS': 4, 'PTRANS': 33, 'TRANS': 445} Chain breaks: 1 Chain: "C" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3381 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5639 Classifications: {'peptide': 712} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 678} Chain breaks: 10 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5455 SG CYS A 820 32.399 52.725 121.141 1.00 74.14 S ATOM 5455 SG CYS A 820 32.399 52.725 121.141 1.00 74.14 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PRO A 492 " occ=0.83 ... (5 atoms not shown) pdb=" CD PRO A 492 " occ=0.83 Time building chain proxies: 4.72, per 1000 atoms: 0.26 Number of scatterers: 18276 At special positions: 0 Unit cell: (101.088, 115.344, 177.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 127 16.00 O 3377 8.00 N 3094 7.00 C 11676 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: 2.11 Conformation dependent library (CDL) restraints added in 969.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 700 " pdb="ZN ZN C 700 " - pdb=" ND1 HIS C 70 " pdb="ZN ZN C 700 " - pdb=" NE2 HIS C 68 " pdb="ZN ZN C 700 " - pdb=" SG CYS A 820 " pdb="ZN ZN C 700 " - pdb=" NE2 HIS C 157 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 414 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS A 820 " Number of angles added : 3 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 45.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.864A pdb=" N SER A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 removed outlier: 4.284A pdb=" N ALA A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 Processing helix chain 'A' and resid 211 through 227 removed outlier: 4.751A pdb=" N GLY A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.166A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Proline residue: A 242 - end of helix Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 310 through 327 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.590A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.731A pdb=" N VAL A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 478 removed outlier: 3.979A pdb=" N LYS A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 514 through 530 removed outlier: 4.141A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 547 through 553 removed outlier: 4.336A pdb=" N GLN A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 573 Processing helix chain 'A' and resid 590 through 601 removed outlier: 4.530A pdb=" N GLU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 622 removed outlier: 3.834A pdb=" N GLN A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 642 removed outlier: 4.164A pdb=" N ALA A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 713 through 732 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 127 through 144 Processing helix chain 'B' and resid 159 through 162 No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.567A pdb=" N GLU B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.532A pdb=" N ALA C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Proline residue: C 101 - end of helix removed outlier: 3.875A pdb=" N LYS C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.690A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 229 Processing helix chain 'C' and resid 246 through 257 removed outlier: 4.525A pdb=" N LEU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 359 through 362 No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 417 through 430 removed outlier: 4.031A pdb=" N GLN C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 145 through 158 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 246 through 262 removed outlier: 3.535A pdb=" N SER D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 305 Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 378 through 383 Processing helix chain 'D' and resid 388 through 404 Processing helix chain 'D' and resid 406 through 418 removed outlier: 4.659A pdb=" N ASP D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 437 Processing helix chain 'D' and resid 446 through 453 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'D' and resid 500 through 511 removed outlier: 3.850A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 518 No H-bonds generated for 'chain 'D' and resid 515 through 518' Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 542 through 557 removed outlier: 3.641A pdb=" N THR D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 580 Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 633 through 649 Processing helix chain 'D' and resid 654 through 671 Processing helix chain 'D' and resid 695 through 705 Processing helix chain 'D' and resid 716 through 734 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 857 through 860 No H-bonds generated for 'chain 'D' and resid 857 through 860' 641 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5966 1.34 - 1.46: 3832 1.46 - 1.58: 8673 1.58 - 1.70: 0 1.70 - 1.81: 187 Bond restraints: 18658 Sorted by residual: bond pdb=" CA THR B 35 " pdb=" C THR B 35 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.72e-02 3.38e+03 8.35e+00 bond pdb=" C MET D 561 " pdb=" N PRO D 562 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.44e-02 4.82e+03 2.50e+00 bond pdb=" CA ILE C 201 " pdb=" CB ILE C 201 " ideal model delta sigma weight residual 1.544 1.524 0.019 1.32e-02 5.74e+03 2.13e+00 bond pdb=" C ILE D 875 " pdb=" N HIS D 876 " ideal model delta sigma weight residual 1.326 1.301 0.025 1.84e-02 2.95e+03 1.86e+00 bond pdb=" CA CYS C 19 " pdb=" C CYS C 19 " ideal model delta sigma weight residual 1.529 1.516 0.013 1.04e-02 9.25e+03 1.47e+00 ... (remaining 18653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 24162 1.50 - 3.00: 995 3.00 - 4.49: 115 4.49 - 5.99: 45 5.99 - 7.49: 7 Bond angle restraints: 25324 Sorted by residual: angle pdb=" N VAL A 504 " pdb=" CA VAL A 504 " pdb=" C VAL A 504 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" C VAL B 392 " pdb=" N VAL B 393 " pdb=" CA VAL B 393 " ideal model delta sigma weight residual 122.96 118.60 4.36 9.50e-01 1.11e+00 2.11e+01 angle pdb=" CA TRP C 340 " pdb=" C TRP C 340 " pdb=" N ALA C 341 " ideal model delta sigma weight residual 117.96 123.14 -5.18 1.23e+00 6.61e-01 1.78e+01 angle pdb=" N VAL C 15 " pdb=" CA VAL C 15 " pdb=" C VAL C 15 " ideal model delta sigma weight residual 111.77 107.47 4.30 1.04e+00 9.25e-01 1.71e+01 angle pdb=" N THR A 293 " pdb=" CA THR A 293 " pdb=" C THR A 293 " ideal model delta sigma weight residual 114.56 109.79 4.77 1.27e+00 6.20e-01 1.41e+01 ... (remaining 25319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10058 17.99 - 35.98: 1021 35.98 - 53.97: 172 53.97 - 71.96: 27 71.96 - 89.95: 25 Dihedral angle restraints: 11303 sinusoidal: 4491 harmonic: 6812 Sorted by residual: dihedral pdb=" CA GLY B 396 " pdb=" C GLY B 396 " pdb=" N HIS B 397 " pdb=" CA HIS B 397 " ideal model delta harmonic sigma weight residual 180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA THR C 324 " pdb=" C THR C 324 " pdb=" N PRO C 325 " pdb=" CA PRO C 325 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ASN B 453 " pdb=" C ASN B 453 " pdb=" N PHE B 454 " pdb=" CA PHE B 454 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 11300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1709 0.031 - 0.062: 829 0.062 - 0.093: 246 0.093 - 0.124: 130 0.124 - 0.155: 20 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA VAL B 392 " pdb=" N VAL B 392 " pdb=" C VAL B 392 " pdb=" CB VAL B 392 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA VAL C 158 " pdb=" N VAL C 158 " pdb=" C VAL C 158 " pdb=" CB VAL C 158 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE C 166 " pdb=" N ILE C 166 " pdb=" C ILE C 166 " pdb=" CB ILE C 166 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2931 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 502 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO A 503 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 876 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO D 877 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 877 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 877 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 100 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 101 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " 0.030 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 182 2.53 - 3.13: 15129 3.13 - 3.72: 28798 3.72 - 4.31: 38138 4.31 - 4.90: 61302 Nonbonded interactions: 143549 Sorted by model distance: nonbonded pdb=" OD2 ASP C 178 " pdb="ZN ZN C 700 " model vdw 1.943 2.230 nonbonded pdb=" O LEU D 841 " pdb=" OG SER D 899 " model vdw 2.135 3.040 nonbonded pdb=" O SER A 230 " pdb=" OG1 THR A 233 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" O ARG B 180 " model vdw 2.161 3.040 nonbonded pdb=" O TYR D 917 " pdb=" N GLU D 943 " model vdw 2.169 3.120 ... (remaining 143544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.83 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.007 0.600 18665 Z= 0.247 Angle : 0.733 24.897 25327 Z= 0.406 Chirality : 0.043 0.155 2934 Planarity : 0.005 0.067 3236 Dihedral : 15.084 89.947 6867 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.15), residues: 2290 helix: -1.80 (0.13), residues: 1170 sheet: -2.39 (0.37), residues: 190 loop : -3.28 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 436 TYR 0.018 0.001 TYR D 897 PHE 0.015 0.001 PHE D 837 TRP 0.013 0.001 TRP A 114 HIS 0.006 0.001 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00415 (18658) covalent geometry : angle 0.70467 (25324) hydrogen bonds : bond 0.06120 ( 641) hydrogen bonds : angle 4.92025 ( 1923) metal coordination : bond 0.27942 ( 7) metal coordination : angle 18.63722 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8289 (m-10) cc_final: 0.8020 (m-10) REVERT: A 79 LEU cc_start: 0.9277 (tp) cc_final: 0.9023 (tp) REVERT: A 83 PHE cc_start: 0.8086 (m-80) cc_final: 0.7816 (m-80) REVERT: A 176 MET cc_start: 0.8761 (mtm) cc_final: 0.8273 (mtm) REVERT: A 458 GLU cc_start: 0.7969 (pp20) cc_final: 0.7657 (pp20) REVERT: A 775 MET cc_start: 0.8304 (ppp) cc_final: 0.7941 (ppp) REVERT: A 796 GLU cc_start: 0.7942 (pm20) cc_final: 0.7649 (pm20) REVERT: B 63 PHE cc_start: 0.6606 (p90) cc_final: 0.6312 (p90) REVERT: B 225 TRP cc_start: 0.8943 (m100) cc_final: 0.8658 (m100) REVERT: B 232 GLU cc_start: 0.6999 (tt0) cc_final: 0.6693 (tt0) REVERT: B 317 ASP cc_start: 0.7886 (t0) cc_final: 0.6777 (t0) REVERT: B 409 MET cc_start: 0.8646 (tpt) cc_final: 0.8152 (tpt) REVERT: B 486 MET cc_start: 0.8150 (mmm) cc_final: 0.7717 (mmm) REVERT: B 500 ARG cc_start: 0.7148 (mpp80) cc_final: 0.6900 (mpt-90) REVERT: C 106 ASP cc_start: 0.8777 (t0) cc_final: 0.8106 (t0) REVERT: C 125 MET cc_start: 0.8440 (mtt) cc_final: 0.8156 (mtt) REVERT: C 151 LYS cc_start: 0.7261 (ttpt) cc_final: 0.7060 (ttpp) REVERT: C 196 ARG cc_start: 0.7220 (mtm-85) cc_final: 0.6997 (mpp80) REVERT: C 406 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7590 (tm-30) REVERT: C 428 GLU cc_start: 0.6446 (tt0) cc_final: 0.6100 (tp30) REVERT: C 442 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7191 (mt-10) REVERT: D 284 PHE cc_start: 0.8301 (t80) cc_final: 0.7874 (t80) REVERT: D 430 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8233 (tp-100) REVERT: D 710 MET cc_start: 0.7676 (ttp) cc_final: 0.7348 (tmm) REVERT: D 725 MET cc_start: 0.8264 (mmm) cc_final: 0.8023 (mmm) REVERT: D 726 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7617 (ttp-170) REVERT: D 881 ASP cc_start: 0.8215 (m-30) cc_final: 0.7702 (t0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1589 time to fit residues: 80.2572 Evaluate side-chains 239 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 443 GLN A 717 GLN B 74 HIS B 210 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 94 HIS C 226 HIS C 277 HIS C 367 GLN D 144 ASN D 176 ASN D 197 GLN D 230 HIS D 274 ASN D 403 GLN D 441 ASN D 568 HIS D 582 HIS D 633 GLN D 644 GLN D 723 HIS D 724 HIS ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.166483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122730 restraints weight = 32078.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121832 restraints weight = 20888.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123493 restraints weight = 16174.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123860 restraints weight = 12188.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124134 restraints weight = 11576.195| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18665 Z= 0.138 Angle : 0.615 8.537 25327 Z= 0.306 Chirality : 0.043 0.197 2934 Planarity : 0.005 0.059 3236 Dihedral : 4.560 20.025 2479 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.67 % Allowed : 12.02 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.17), residues: 2290 helix: -0.48 (0.15), residues: 1183 sheet: -2.24 (0.35), residues: 204 loop : -2.45 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 517 TYR 0.020 0.001 TYR C 179 PHE 0.023 0.002 PHE C 221 TRP 0.019 0.001 TRP A 35 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00319 (18658) covalent geometry : angle 0.61491 (25324) hydrogen bonds : bond 0.03496 ( 641) hydrogen bonds : angle 4.29682 ( 1923) metal coordination : bond 0.01747 ( 7) metal coordination : angle 2.47301 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.760 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: A 458 GLU cc_start: 0.7954 (pp20) cc_final: 0.7562 (pp20) REVERT: A 775 MET cc_start: 0.8306 (ppp) cc_final: 0.7951 (ppp) REVERT: B 1 MET cc_start: 0.7728 (mpp) cc_final: 0.7435 (mpp) REVERT: B 63 PHE cc_start: 0.6589 (p90) cc_final: 0.6290 (p90) REVERT: B 317 ASP cc_start: 0.7776 (t0) cc_final: 0.6774 (t0) REVERT: B 409 MET cc_start: 0.8787 (tpt) cc_final: 0.8278 (tpt) REVERT: B 424 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 430 LEU cc_start: 0.7477 (mt) cc_final: 0.7274 (tp) REVERT: B 486 MET cc_start: 0.8104 (mmm) cc_final: 0.7745 (mmm) REVERT: C 151 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6945 (ttpp) REVERT: C 196 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.6964 (mpp80) REVERT: C 231 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5711 (ptt90) REVERT: C 347 MET cc_start: 0.6540 (tmm) cc_final: 0.6051 (tmm) REVERT: C 382 MET cc_start: 0.7525 (mtm) cc_final: 0.7221 (mpp) REVERT: C 387 MET cc_start: 0.7777 (mmm) cc_final: 0.7548 (mmm) REVERT: C 406 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7554 (tm-30) REVERT: C 428 GLU cc_start: 0.6602 (tt0) cc_final: 0.6301 (tp30) REVERT: C 442 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7024 (mt-10) REVERT: D 92 ILE cc_start: 0.8300 (mm) cc_final: 0.8063 (mt) REVERT: D 173 LEU cc_start: 0.9310 (tp) cc_final: 0.8992 (mm) REVERT: D 379 PHE cc_start: 0.7746 (m-80) cc_final: 0.7210 (m-80) REVERT: D 415 PHE cc_start: 0.8725 (m-80) cc_final: 0.8144 (m-80) REVERT: D 430 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8276 (tp-100) REVERT: D 710 MET cc_start: 0.7531 (ttp) cc_final: 0.7291 (tmm) REVERT: D 725 MET cc_start: 0.8361 (mmm) cc_final: 0.8141 (mmm) outliers start: 34 outliers final: 16 residues processed: 311 average time/residue: 0.1377 time to fit residues: 66.9454 Evaluate side-chains 255 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 224 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 130 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 389 GLN C 137 HIS C 165 GLN D 221 GLN D 274 ASN D 572 HIS D 728 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.166464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122881 restraints weight = 32091.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121519 restraints weight = 21646.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123397 restraints weight = 16985.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123757 restraints weight = 13395.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124230 restraints weight = 11428.539| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18665 Z= 0.132 Angle : 0.591 8.539 25327 Z= 0.292 Chirality : 0.042 0.158 2934 Planarity : 0.004 0.057 3236 Dihedral : 4.397 20.255 2479 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.02 % Allowed : 14.38 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.18), residues: 2290 helix: -0.06 (0.15), residues: 1182 sheet: -1.70 (0.36), residues: 211 loop : -2.13 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.019 0.001 TYR C 86 PHE 0.022 0.001 PHE C 221 TRP 0.009 0.001 TRP A 232 HIS 0.007 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00309 (18658) covalent geometry : angle 0.59016 (25324) hydrogen bonds : bond 0.03353 ( 641) hydrogen bonds : angle 4.16247 ( 1923) metal coordination : bond 0.01744 ( 7) metal coordination : angle 2.60529 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.801 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: A 140 LEU cc_start: 0.8855 (mt) cc_final: 0.8488 (mt) REVERT: A 218 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 458 GLU cc_start: 0.7943 (pp20) cc_final: 0.7713 (pp20) REVERT: A 569 MET cc_start: 0.8804 (mmm) cc_final: 0.8399 (mmm) REVERT: A 796 GLU cc_start: 0.7692 (pm20) cc_final: 0.7486 (pm20) REVERT: B 32 MET cc_start: 0.7922 (ttm) cc_final: 0.7679 (ttm) REVERT: B 63 PHE cc_start: 0.6633 (p90) cc_final: 0.6337 (p90) REVERT: B 317 ASP cc_start: 0.7777 (t0) cc_final: 0.6763 (t0) REVERT: B 409 MET cc_start: 0.8761 (tpt) cc_final: 0.8190 (tpt) REVERT: B 424 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 486 MET cc_start: 0.8102 (mmm) cc_final: 0.7747 (mmm) REVERT: C 148 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7612 (mp) REVERT: C 231 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.5054 (ptt90) REVERT: C 347 MET cc_start: 0.6606 (tmm) cc_final: 0.6052 (tmm) REVERT: C 361 HIS cc_start: 0.7172 (t-90) cc_final: 0.6758 (t70) REVERT: C 382 MET cc_start: 0.7531 (mtm) cc_final: 0.7091 (mpp) REVERT: C 387 MET cc_start: 0.7802 (mmm) cc_final: 0.7588 (mmm) REVERT: C 406 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7557 (tp30) REVERT: C 428 GLU cc_start: 0.6635 (tt0) cc_final: 0.6215 (tp30) REVERT: C 442 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7053 (mt-10) REVERT: D 92 ILE cc_start: 0.8292 (mm) cc_final: 0.8056 (mt) REVERT: D 173 LEU cc_start: 0.9371 (tp) cc_final: 0.9098 (mm) REVERT: D 379 PHE cc_start: 0.7799 (m-80) cc_final: 0.7563 (m-80) REVERT: D 415 PHE cc_start: 0.8725 (m-80) cc_final: 0.8078 (m-80) REVERT: D 430 GLN cc_start: 0.8444 (tp-100) cc_final: 0.7919 (tp-100) REVERT: D 710 MET cc_start: 0.7485 (ttp) cc_final: 0.6852 (tmm) REVERT: D 881 ASP cc_start: 0.8144 (m-30) cc_final: 0.7614 (t0) outliers start: 41 outliers final: 17 residues processed: 302 average time/residue: 0.1297 time to fit residues: 62.1904 Evaluate side-chains 259 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 0.0010 chunk 47 optimal weight: 0.8980 chunk 123 optimal weight: 0.0070 chunk 28 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125625 restraints weight = 32001.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123900 restraints weight = 21478.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125353 restraints weight = 16560.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125929 restraints weight = 12851.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126195 restraints weight = 11622.897| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18665 Z= 0.104 Angle : 0.568 8.634 25327 Z= 0.278 Chirality : 0.042 0.185 2934 Planarity : 0.004 0.057 3236 Dihedral : 4.186 20.230 2479 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.17 % Allowed : 16.06 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.18), residues: 2290 helix: 0.22 (0.16), residues: 1179 sheet: -1.29 (0.36), residues: 211 loop : -1.88 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.016 0.001 TYR C 278 PHE 0.017 0.001 PHE C 221 TRP 0.010 0.001 TRP B 225 HIS 0.009 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00234 (18658) covalent geometry : angle 0.56782 (25324) hydrogen bonds : bond 0.03110 ( 641) hydrogen bonds : angle 4.00533 ( 1923) metal coordination : bond 0.01352 ( 7) metal coordination : angle 1.79443 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.749 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: A 140 LEU cc_start: 0.8950 (mt) cc_final: 0.8632 (mt) REVERT: A 458 GLU cc_start: 0.7682 (pp20) cc_final: 0.7297 (pp20) REVERT: A 569 MET cc_start: 0.8759 (mmm) cc_final: 0.8369 (mmm) REVERT: B 63 PHE cc_start: 0.6724 (p90) cc_final: 0.6436 (p90) REVERT: B 225 TRP cc_start: 0.8853 (m100) cc_final: 0.8588 (m100) REVERT: B 317 ASP cc_start: 0.7854 (t0) cc_final: 0.6948 (t0) REVERT: B 409 MET cc_start: 0.8757 (tpt) cc_final: 0.8200 (tpt) REVERT: B 486 MET cc_start: 0.8074 (mmm) cc_final: 0.7805 (mmm) REVERT: C 347 MET cc_start: 0.6777 (tmm) cc_final: 0.6231 (tmm) REVERT: C 361 HIS cc_start: 0.7038 (t-90) cc_final: 0.6265 (t-90) REVERT: C 382 MET cc_start: 0.7436 (mtm) cc_final: 0.6935 (mpp) REVERT: C 406 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7589 (tp30) REVERT: C 428 GLU cc_start: 0.6542 (tt0) cc_final: 0.6267 (tp30) REVERT: C 442 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7041 (mt-10) REVERT: D 92 ILE cc_start: 0.8295 (mm) cc_final: 0.8082 (mt) REVERT: D 173 LEU cc_start: 0.9302 (tp) cc_final: 0.9069 (mm) REVERT: D 379 PHE cc_start: 0.7968 (m-80) cc_final: 0.7651 (m-80) REVERT: D 415 PHE cc_start: 0.8743 (m-80) cc_final: 0.8145 (m-80) REVERT: D 430 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8036 (tp-100) REVERT: D 710 MET cc_start: 0.7462 (ttp) cc_final: 0.6793 (tmm) REVERT: D 881 ASP cc_start: 0.8108 (m-30) cc_final: 0.7501 (t0) outliers start: 44 outliers final: 22 residues processed: 302 average time/residue: 0.1228 time to fit residues: 59.9784 Evaluate side-chains 257 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 104 optimal weight: 0.0870 chunk 142 optimal weight: 0.4980 chunk 6 optimal weight: 0.0770 chunk 190 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 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 = 0.4168 r_free = 0.4168 target = 0.170457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127270 restraints weight = 31584.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126003 restraints weight = 23102.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127535 restraints weight = 20117.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128764 restraints weight = 14042.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129915 restraints weight = 11985.967| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18665 Z= 0.100 Angle : 0.566 10.255 25327 Z= 0.273 Chirality : 0.041 0.247 2934 Planarity : 0.004 0.059 3236 Dihedral : 3.979 19.545 2479 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.97 % Allowed : 16.85 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.18), residues: 2290 helix: 0.39 (0.16), residues: 1187 sheet: -0.97 (0.37), residues: 202 loop : -1.62 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.016 0.001 TYR C 278 PHE 0.020 0.001 PHE C 221 TRP 0.015 0.001 TRP A 35 HIS 0.007 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00227 (18658) covalent geometry : angle 0.56552 (25324) hydrogen bonds : bond 0.02962 ( 641) hydrogen bonds : angle 3.86456 ( 1923) metal coordination : bond 0.01249 ( 7) metal coordination : angle 1.29219 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.772 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: A 36 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: A 140 LEU cc_start: 0.9018 (mt) cc_final: 0.8722 (mt) REVERT: A 458 GLU cc_start: 0.7627 (pp20) cc_final: 0.7281 (pp20) REVERT: A 569 MET cc_start: 0.8727 (mmm) cc_final: 0.8337 (mmm) REVERT: A 796 GLU cc_start: 0.7636 (pm20) cc_final: 0.7379 (pm20) REVERT: A 806 MET cc_start: 0.7215 (tpt) cc_final: 0.6958 (tpt) REVERT: B 55 TRP cc_start: 0.7944 (t60) cc_final: 0.7682 (t60) REVERT: B 63 PHE cc_start: 0.6678 (p90) cc_final: 0.6427 (p90) REVERT: B 157 LYS cc_start: 0.7251 (mmtm) cc_final: 0.6911 (mmtm) REVERT: B 225 TRP cc_start: 0.8736 (m100) cc_final: 0.8509 (m100) REVERT: B 317 ASP cc_start: 0.7887 (t0) cc_final: 0.6986 (t0) REVERT: B 409 MET cc_start: 0.8675 (tpt) cc_final: 0.8084 (tpt) REVERT: B 499 TYR cc_start: 0.7879 (p90) cc_final: 0.7538 (p90) REVERT: C 231 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5431 (ptt90) REVERT: C 347 MET cc_start: 0.6579 (tmm) cc_final: 0.6103 (tmm) REVERT: C 361 HIS cc_start: 0.6993 (t-90) cc_final: 0.6285 (t-90) REVERT: C 382 MET cc_start: 0.7533 (mtm) cc_final: 0.7010 (mpp) REVERT: C 406 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7662 (tp30) REVERT: C 442 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6983 (mt-10) REVERT: D 127 LEU cc_start: 0.8027 (mp) cc_final: 0.7583 (tp) REVERT: D 169 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8215 (tppt) REVERT: D 173 LEU cc_start: 0.9290 (tp) cc_final: 0.9062 (mm) REVERT: D 415 PHE cc_start: 0.8720 (m-80) cc_final: 0.8165 (m-80) REVERT: D 430 GLN cc_start: 0.8355 (tp-100) cc_final: 0.8026 (tp-100) REVERT: D 710 MET cc_start: 0.7381 (ttp) cc_final: 0.6776 (tmm) REVERT: D 881 ASP cc_start: 0.8044 (m-30) cc_final: 0.7446 (t0) outliers start: 40 outliers final: 20 residues processed: 294 average time/residue: 0.1245 time to fit residues: 59.4289 Evaluate side-chains 265 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 553 ASN ** 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 = 0.4162 r_free = 0.4162 target = 0.169695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126449 restraints weight = 31476.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125753 restraints weight = 22016.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127006 restraints weight = 18579.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127422 restraints weight = 14571.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127923 restraints weight = 12190.293| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18665 Z= 0.108 Angle : 0.584 15.194 25327 Z= 0.276 Chirality : 0.042 0.265 2934 Planarity : 0.004 0.057 3236 Dihedral : 3.913 18.764 2479 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.17 % Allowed : 18.03 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.18), residues: 2290 helix: 0.50 (0.16), residues: 1187 sheet: -0.78 (0.38), residues: 202 loop : -1.48 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.012 0.001 TYR C 179 PHE 0.019 0.001 PHE C 221 TRP 0.025 0.001 TRP A 35 HIS 0.011 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00250 (18658) covalent geometry : angle 0.58418 (25324) hydrogen bonds : bond 0.02936 ( 641) hydrogen bonds : angle 3.80826 ( 1923) metal coordination : bond 0.01259 ( 7) metal coordination : angle 0.96438 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.802 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: A 458 GLU cc_start: 0.7567 (pp20) cc_final: 0.7223 (pp20) REVERT: A 569 MET cc_start: 0.8749 (mmm) cc_final: 0.8392 (mmm) REVERT: A 806 MET cc_start: 0.7208 (tpt) cc_final: 0.6961 (tpt) REVERT: B 55 TRP cc_start: 0.7940 (t60) cc_final: 0.7678 (t60) REVERT: B 157 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6949 (mmtm) REVERT: B 225 TRP cc_start: 0.8762 (m100) cc_final: 0.8511 (m100) REVERT: B 317 ASP cc_start: 0.7903 (t0) cc_final: 0.7004 (t0) REVERT: B 409 MET cc_start: 0.8705 (tpt) cc_final: 0.8116 (tpt) REVERT: B 499 TYR cc_start: 0.7869 (p90) cc_final: 0.7548 (p90) REVERT: C 163 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6084 (mmt) REVERT: C 231 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5291 (ptt90) REVERT: C 347 MET cc_start: 0.6679 (tmm) cc_final: 0.6306 (tmm) REVERT: C 361 HIS cc_start: 0.6957 (t-90) cc_final: 0.6431 (t70) REVERT: C 382 MET cc_start: 0.7456 (mtm) cc_final: 0.7252 (mpp) REVERT: C 406 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7634 (tp30) REVERT: C 442 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7022 (mt-10) REVERT: D 127 LEU cc_start: 0.8109 (mp) cc_final: 0.7604 (tp) REVERT: D 169 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8195 (tppt) REVERT: D 173 LEU cc_start: 0.9289 (tp) cc_final: 0.9014 (mm) REVERT: D 415 PHE cc_start: 0.8696 (m-80) cc_final: 0.8146 (m-80) REVERT: D 430 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8012 (tp-100) REVERT: D 710 MET cc_start: 0.7383 (ttp) cc_final: 0.6791 (tmm) REVERT: D 881 ASP cc_start: 0.7978 (m-30) cc_final: 0.7392 (t0) outliers start: 44 outliers final: 28 residues processed: 286 average time/residue: 0.1279 time to fit residues: 59.2590 Evaluate side-chains 270 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 230 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 172 optimal weight: 50.0000 chunk 218 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 63 optimal weight: 0.0000 chunk 130 optimal weight: 3.9990 chunk 214 optimal weight: 20.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** 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 = 0.4153 r_free = 0.4153 target = 0.168577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125154 restraints weight = 31750.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124426 restraints weight = 21000.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125796 restraints weight = 16055.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126260 restraints weight = 13382.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126902 restraints weight = 11190.220| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18665 Z= 0.133 Angle : 0.603 14.046 25327 Z= 0.288 Chirality : 0.043 0.334 2934 Planarity : 0.004 0.057 3236 Dihedral : 3.968 19.476 2479 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.12 % Allowed : 19.31 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.18), residues: 2290 helix: 0.51 (0.16), residues: 1180 sheet: -0.85 (0.37), residues: 212 loop : -1.41 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 836 TYR 0.015 0.001 TYR C 179 PHE 0.028 0.001 PHE B 63 TRP 0.037 0.001 TRP A 35 HIS 0.012 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00311 (18658) covalent geometry : angle 0.60275 (25324) hydrogen bonds : bond 0.03015 ( 641) hydrogen bonds : angle 3.87911 ( 1923) metal coordination : bond 0.01030 ( 7) metal coordination : angle 1.25972 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.788 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: A 458 GLU cc_start: 0.7640 (pp20) cc_final: 0.7365 (pp20) REVERT: A 569 MET cc_start: 0.8752 (mmm) cc_final: 0.8392 (mmm) REVERT: A 796 GLU cc_start: 0.7425 (pm20) cc_final: 0.7106 (pm20) REVERT: A 806 MET cc_start: 0.7254 (tpt) cc_final: 0.6963 (tpt) REVERT: B 119 PHE cc_start: 0.8481 (t80) cc_final: 0.8026 (t80) REVERT: B 225 TRP cc_start: 0.8876 (m100) cc_final: 0.8571 (m100) REVERT: B 317 ASP cc_start: 0.7884 (t0) cc_final: 0.6969 (t0) REVERT: B 339 PHE cc_start: 0.5903 (m-10) cc_final: 0.5607 (m-10) REVERT: B 409 MET cc_start: 0.8722 (tpt) cc_final: 0.8100 (tpt) REVERT: B 499 TYR cc_start: 0.7939 (p90) cc_final: 0.7534 (p90) REVERT: C 113 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: C 181 MET cc_start: 0.7223 (mmm) cc_final: 0.6960 (mmm) REVERT: C 231 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5293 (ptt90) REVERT: C 347 MET cc_start: 0.6708 (tmm) cc_final: 0.6314 (tmm) REVERT: C 361 HIS cc_start: 0.7002 (t-90) cc_final: 0.6314 (t-90) REVERT: C 382 MET cc_start: 0.7485 (mtm) cc_final: 0.7053 (mpp) REVERT: C 406 GLU cc_start: 0.8057 (mm-30) cc_final: 0.6920 (mm-30) REVERT: C 442 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7065 (mt-10) REVERT: D 127 LEU cc_start: 0.8099 (mp) cc_final: 0.7630 (tp) REVERT: D 169 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8154 (tppt) REVERT: D 173 LEU cc_start: 0.9299 (tp) cc_final: 0.9020 (mm) REVERT: D 415 PHE cc_start: 0.8718 (m-80) cc_final: 0.8073 (m-80) REVERT: D 430 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8045 (tp-100) REVERT: D 710 MET cc_start: 0.7431 (ttp) cc_final: 0.6817 (tmm) REVERT: D 881 ASP cc_start: 0.8018 (m-30) cc_final: 0.7389 (t0) outliers start: 43 outliers final: 32 residues processed: 282 average time/residue: 0.1288 time to fit residues: 58.2684 Evaluate side-chains 272 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.0170 chunk 148 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 164 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 HIS ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.168455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124941 restraints weight = 31733.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124594 restraints weight = 21423.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125638 restraints weight = 16182.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126217 restraints weight = 13411.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126595 restraints weight = 11465.684| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18665 Z= 0.127 Angle : 0.603 14.525 25327 Z= 0.289 Chirality : 0.043 0.381 2934 Planarity : 0.004 0.057 3236 Dihedral : 3.992 18.773 2479 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 19.66 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2290 helix: 0.54 (0.16), residues: 1178 sheet: -0.85 (0.37), residues: 212 loop : -1.33 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 196 TYR 0.022 0.001 TYR C 353 PHE 0.043 0.001 PHE B 63 TRP 0.047 0.001 TRP A 35 HIS 0.014 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00296 (18658) covalent geometry : angle 0.60266 (25324) hydrogen bonds : bond 0.02978 ( 641) hydrogen bonds : angle 3.89888 ( 1923) metal coordination : bond 0.00816 ( 7) metal coordination : angle 1.81800 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 GLU cc_start: 0.7618 (pp20) cc_final: 0.7350 (pp20) REVERT: A 569 MET cc_start: 0.8751 (mmm) cc_final: 0.8377 (mmm) REVERT: B 157 LYS cc_start: 0.7373 (mmtt) cc_final: 0.7040 (mmtm) REVERT: B 225 TRP cc_start: 0.8854 (m100) cc_final: 0.8649 (m100) REVERT: B 317 ASP cc_start: 0.7874 (t0) cc_final: 0.6950 (t0) REVERT: B 409 MET cc_start: 0.8691 (tpt) cc_final: 0.8137 (tpt) REVERT: B 499 TYR cc_start: 0.8012 (p90) cc_final: 0.7640 (p90) REVERT: C 113 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: C 151 LYS cc_start: 0.7413 (tttm) cc_final: 0.7141 (ttpp) REVERT: C 181 MET cc_start: 0.7333 (mmm) cc_final: 0.7125 (mmm) REVERT: C 231 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.5260 (ptt90) REVERT: C 347 MET cc_start: 0.6718 (tmm) cc_final: 0.6337 (tmm) REVERT: C 361 HIS cc_start: 0.7018 (t-90) cc_final: 0.6312 (t-90) REVERT: C 382 MET cc_start: 0.7479 (mtm) cc_final: 0.7154 (mpp) REVERT: C 442 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7043 (mt-10) REVERT: D 127 LEU cc_start: 0.8204 (mp) cc_final: 0.7776 (tp) REVERT: D 169 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8146 (tppt) REVERT: D 173 LEU cc_start: 0.9287 (tp) cc_final: 0.9018 (mm) REVERT: D 389 GLU cc_start: 0.8356 (mp0) cc_final: 0.8046 (mp0) REVERT: D 400 MET cc_start: 0.7757 (tpp) cc_final: 0.7381 (tpp) REVERT: D 415 PHE cc_start: 0.8691 (m-80) cc_final: 0.8188 (m-80) REVERT: D 561 MET cc_start: 0.0853 (mtm) cc_final: -0.0675 (mmm) REVERT: D 710 MET cc_start: 0.7409 (ttp) cc_final: 0.6823 (tmm) REVERT: D 733 GLN cc_start: 0.5739 (pp30) cc_final: 0.5502 (pp30) REVERT: D 881 ASP cc_start: 0.7993 (m-30) cc_final: 0.7370 (t0) outliers start: 41 outliers final: 31 residues processed: 285 average time/residue: 0.1259 time to fit residues: 57.8437 Evaluate side-chains 278 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** 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 = 0.4157 r_free = 0.4157 target = 0.168916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125562 restraints weight = 31709.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124780 restraints weight = 20888.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125962 restraints weight = 16336.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126568 restraints weight = 13420.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127298 restraints weight = 11324.145| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18665 Z= 0.124 Angle : 0.604 9.958 25327 Z= 0.290 Chirality : 0.042 0.196 2934 Planarity : 0.004 0.056 3236 Dihedral : 3.980 18.895 2479 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.92 % Allowed : 20.39 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2290 helix: 0.59 (0.16), residues: 1178 sheet: -0.83 (0.37), residues: 212 loop : -1.30 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 163 TYR 0.021 0.001 TYR C 353 PHE 0.040 0.001 PHE B 63 TRP 0.043 0.001 TRP A 35 HIS 0.014 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00292 (18658) covalent geometry : angle 0.60308 (25324) hydrogen bonds : bond 0.02975 ( 641) hydrogen bonds : angle 3.88761 ( 1923) metal coordination : bond 0.00620 ( 7) metal coordination : angle 2.33519 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 GLU cc_start: 0.7670 (pp20) cc_final: 0.7223 (pp20) REVERT: A 569 MET cc_start: 0.8754 (mmm) cc_final: 0.8363 (mmm) REVERT: B 157 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6965 (mmtm) REVERT: B 199 TYR cc_start: 0.7656 (m-80) cc_final: 0.7423 (m-80) REVERT: B 225 TRP cc_start: 0.8880 (m100) cc_final: 0.8647 (m100) REVERT: B 317 ASP cc_start: 0.7943 (t0) cc_final: 0.6979 (t0) REVERT: B 409 MET cc_start: 0.8676 (tpt) cc_final: 0.8036 (tpt) REVERT: B 499 TYR cc_start: 0.8016 (p90) cc_final: 0.7626 (p90) REVERT: C 113 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: C 163 MET cc_start: 0.6107 (mmt) cc_final: 0.5392 (mmt) REVERT: C 231 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5225 (ptt90) REVERT: C 347 MET cc_start: 0.6714 (tmm) cc_final: 0.6296 (tmm) REVERT: C 361 HIS cc_start: 0.7024 (t-90) cc_final: 0.6309 (t-90) REVERT: C 382 MET cc_start: 0.7469 (mtm) cc_final: 0.7142 (mpp) REVERT: C 420 MET cc_start: 0.6087 (mtt) cc_final: 0.5772 (mtm) REVERT: C 442 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7049 (mt-10) REVERT: D 127 LEU cc_start: 0.8205 (mp) cc_final: 0.7789 (tp) REVERT: D 169 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8136 (tppt) REVERT: D 173 LEU cc_start: 0.9306 (tp) cc_final: 0.9031 (mm) REVERT: D 389 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: D 415 PHE cc_start: 0.8681 (m-80) cc_final: 0.8193 (m-80) REVERT: D 430 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8040 (tp-100) REVERT: D 561 MET cc_start: 0.0347 (mtm) cc_final: -0.0912 (mmm) REVERT: D 707 MET cc_start: 0.6343 (ttt) cc_final: 0.5804 (ptm) REVERT: D 710 MET cc_start: 0.7416 (ttp) cc_final: 0.6683 (tmm) REVERT: D 881 ASP cc_start: 0.7992 (m-30) cc_final: 0.7374 (t0) outliers start: 39 outliers final: 33 residues processed: 281 average time/residue: 0.1191 time to fit residues: 54.3869 Evaluate side-chains 278 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 37 optimal weight: 0.0020 chunk 171 optimal weight: 3.9990 chunk 219 optimal weight: 0.0030 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN B 45 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.169814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126646 restraints weight = 31868.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126021 restraints weight = 21732.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126924 restraints weight = 16579.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127610 restraints weight = 13187.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127872 restraints weight = 11806.878| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18665 Z= 0.116 Angle : 0.620 10.872 25327 Z= 0.295 Chirality : 0.042 0.202 2934 Planarity : 0.004 0.057 3236 Dihedral : 3.931 18.824 2479 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.82 % Allowed : 20.74 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2290 helix: 0.63 (0.16), residues: 1177 sheet: -0.77 (0.37), residues: 212 loop : -1.23 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 163 TYR 0.023 0.001 TYR C 353 PHE 0.047 0.001 PHE B 63 TRP 0.043 0.001 TRP A 35 HIS 0.028 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00269 (18658) covalent geometry : angle 0.61960 (25324) hydrogen bonds : bond 0.02916 ( 641) hydrogen bonds : angle 3.87574 ( 1923) metal coordination : bond 0.00743 ( 7) metal coordination : angle 3.04713 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 GLU cc_start: 0.7562 (pp20) cc_final: 0.7226 (pp20) REVERT: A 569 MET cc_start: 0.8685 (mmm) cc_final: 0.8363 (mmm) REVERT: B 157 LYS cc_start: 0.7236 (mmtt) cc_final: 0.7000 (mmtm) REVERT: B 199 TYR cc_start: 0.7648 (m-80) cc_final: 0.7443 (m-80) REVERT: B 317 ASP cc_start: 0.7930 (t0) cc_final: 0.6986 (t0) REVERT: B 409 MET cc_start: 0.8689 (tpt) cc_final: 0.8076 (tpt) REVERT: C 113 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: C 151 LYS cc_start: 0.7407 (tttm) cc_final: 0.7175 (ptmm) REVERT: C 163 MET cc_start: 0.6382 (mmt) cc_final: 0.5684 (mmt) REVERT: C 231 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5144 (ptt90) REVERT: C 347 MET cc_start: 0.6734 (tmm) cc_final: 0.6315 (tmm) REVERT: C 361 HIS cc_start: 0.6973 (t-90) cc_final: 0.6245 (t-90) REVERT: C 382 MET cc_start: 0.7435 (mtm) cc_final: 0.7115 (mpp) REVERT: C 420 MET cc_start: 0.6078 (mtt) cc_final: 0.5741 (mtm) REVERT: C 442 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7025 (mt-10) REVERT: D 127 LEU cc_start: 0.8161 (mp) cc_final: 0.7766 (tp) REVERT: D 169 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8133 (tppt) REVERT: D 173 LEU cc_start: 0.9288 (tp) cc_final: 0.9024 (mm) REVERT: D 415 PHE cc_start: 0.8623 (m-80) cc_final: 0.8207 (m-80) REVERT: D 430 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8002 (tp-100) REVERT: D 561 MET cc_start: 0.0485 (mtm) cc_final: -0.0705 (mmm) REVERT: D 710 MET cc_start: 0.7404 (ttp) cc_final: 0.6679 (tmm) REVERT: D 881 ASP cc_start: 0.7952 (m-30) cc_final: 0.7367 (t0) outliers start: 37 outliers final: 31 residues processed: 278 average time/residue: 0.1298 time to fit residues: 57.8442 Evaluate side-chains 273 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 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 = 0.4151 r_free = 0.4151 target = 0.171615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125421 restraints weight = 32406.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124391 restraints weight = 20494.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125567 restraints weight = 15222.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126138 restraints weight = 12895.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126505 restraints weight = 11754.451| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18665 Z= 0.137 Angle : 0.630 11.838 25327 Z= 0.302 Chirality : 0.043 0.236 2934 Planarity : 0.004 0.057 3236 Dihedral : 4.012 20.394 2479 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.77 % Allowed : 20.69 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2290 helix: 0.66 (0.16), residues: 1176 sheet: -0.82 (0.37), residues: 214 loop : -1.23 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 163 TYR 0.029 0.001 TYR C 353 PHE 0.049 0.002 PHE B 63 TRP 0.053 0.002 TRP A 35 HIS 0.017 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00325 (18658) covalent geometry : angle 0.62925 (25324) hydrogen bonds : bond 0.03013 ( 641) hydrogen bonds : angle 3.95954 ( 1923) metal coordination : bond 0.00733 ( 7) metal coordination : angle 2.81758 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.46 seconds wall clock time: 53 minutes 44.14 seconds (3224.14 seconds total)