Starting phenix.real_space_refine on Mon Jun 16 05:42:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2d_18839/06_2025/8r2d_18839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2d_18839/06_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_18839/06_2025/8r2d_18839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2d_18839/06_2025/8r2d_18839.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2d_18839/06_2025/8r2d_18839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2d_18839/06_2025/8r2d_18839.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP: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: 11.38, per 1000 atoms: 0.62 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: 5.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.51 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: 4.36 Time building geometry restraints manager: 5.66 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- 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 : 14.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP A 114 HIS 0.006 0.001 HIS D 223 PHE 0.015 0.001 PHE D 837 TYR 0.018 0.001 TYR D 897 ARG 0.004 0.000 ARG D 436 Details of bonding type rmsd hydrogen bonds : bond 0.06120 ( 641) hydrogen bonds : angle 4.92025 ( 1923) metal coordination : bond 0.27942 ( 7) metal coordination : angle 18.63722 ( 3) covalent geometry : bond 0.00415 (18658) covalent geometry : angle 0.70467 (25324) *********************** 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 : 2.203 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: 0.9024 (tp) REVERT: A 83 PHE cc_start: 0.8086 (m-80) cc_final: 0.7815 (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: 0.7658 (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: 0.7648 (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: 0.6691 (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: 0.8153 (tpt) REVERT: B 486 MET cc_start: 0.8150 (mmm) cc_final: 0.7739 (mmm) REVERT: B 500 ARG cc_start: 0.7148 (mpp80) cc_final: 0.6899 (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: 0.8155 (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: 0.6101 (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: 0.7873 (t80) REVERT: D 430 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8228 (tp-100) REVERT: D 710 MET cc_start: 0.7676 (ttp) cc_final: 0.7345 (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: 0.7711 (t0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3257 time to fit residues: 164.2811 Evaluate side-chains 241 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 426 GLN A 443 GLN A 548 GLN B 74 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 97 GLN C 137 HIS C 165 GLN C 226 HIS ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 144 ASN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 HIS ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 GLN D 441 ASN D 568 HIS ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 GLN D 644 GLN ** D 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 HIS ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.160723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118214 restraints weight = 32631.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115090 restraints weight = 23570.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116864 restraints weight = 20479.242| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 18665 Z= 0.295 Angle : 0.749 9.363 25327 Z= 0.372 Chirality : 0.047 0.182 2934 Planarity : 0.006 0.066 3236 Dihedral : 5.118 28.874 2479 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.32 % Allowed : 14.43 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.17), residues: 2290 helix: -0.79 (0.14), residues: 1174 sheet: -2.42 (0.34), residues: 227 loop : -2.80 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 35 HIS 0.008 0.002 HIS A 61 PHE 0.027 0.002 PHE D 379 TYR 0.037 0.002 TYR C 179 ARG 0.006 0.001 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 641) hydrogen bonds : angle 4.76190 ( 1923) metal coordination : bond 0.02319 ( 7) metal coordination : angle 4.51409 ( 3) covalent geometry : bond 0.00688 (18658) covalent geometry : angle 0.74697 (25324) *********************** 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 319 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 1.982 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 79 LEU cc_start: 0.9369 (tp) cc_final: 0.9043 (tp) REVERT: A 83 PHE cc_start: 0.8165 (m-80) cc_final: 0.7824 (m-80) REVERT: A 458 GLU cc_start: 0.8127 (pp20) cc_final: 0.7901 (pp20) REVERT: B 19 PHE cc_start: 0.7278 (t80) cc_final: 0.6956 (t80) REVERT: B 63 PHE cc_start: 0.6676 (p90) cc_final: 0.6415 (p90) REVERT: B 317 ASP cc_start: 0.7956 (t0) cc_final: 0.6795 (t0) REVERT: B 409 MET cc_start: 0.8678 (tpt) cc_final: 0.8148 (tpt) REVERT: B 424 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 430 LEU cc_start: 0.7923 (mt) cc_final: 0.7668 (tp) REVERT: B 486 MET cc_start: 0.8098 (mmm) cc_final: 0.7736 (mmm) REVERT: C 86 TYR cc_start: 0.9197 (t80) cc_final: 0.8949 (t80) REVERT: C 106 ASP cc_start: 0.8786 (t0) cc_final: 0.8130 (t0) REVERT: C 113 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: C 196 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6919 (mtm180) REVERT: C 347 MET cc_start: 0.6726 (tmm) cc_final: 0.6395 (tmm) REVERT: C 350 MET cc_start: 0.7978 (mmm) cc_final: 0.7758 (mmm) REVERT: C 382 MET cc_start: 0.7717 (mtm) cc_final: 0.7370 (mpp) REVERT: C 442 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 173 LEU cc_start: 0.9380 (tp) cc_final: 0.9094 (mm) REVERT: D 379 PHE cc_start: 0.7792 (m-80) cc_final: 0.7251 (m-80) REVERT: D 415 PHE cc_start: 0.8715 (m-80) cc_final: 0.8160 (m-80) REVERT: D 710 MET cc_start: 0.7525 (ttp) cc_final: 0.7283 (tmm) REVERT: D 725 MET cc_start: 0.8299 (mmm) cc_final: 0.8045 (mmm) outliers start: 47 outliers final: 28 residues processed: 298 average time/residue: 0.2839 time to fit residues: 131.9872 Evaluate side-chains 259 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 123 VAL 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 231 TYR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 443 THR 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 68 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 146 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 443 GLN B 210 GLN C 277 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 572 HIS D 582 HIS ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.165380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121698 restraints weight = 31905.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120656 restraints weight = 20148.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122178 restraints weight = 16709.715| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18665 Z= 0.134 Angle : 0.609 8.605 25327 Z= 0.301 Chirality : 0.043 0.218 2934 Planarity : 0.005 0.059 3236 Dihedral : 4.628 21.561 2479 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.61 % Allowed : 15.76 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 2290 helix: -0.21 (0.15), residues: 1183 sheet: -1.76 (0.37), residues: 203 loop : -2.29 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 114 HIS 0.012 0.001 HIS D 723 PHE 0.021 0.001 PHE C 221 TYR 0.017 0.001 TYR C 278 ARG 0.006 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 641) hydrogen bonds : angle 4.30259 ( 1923) metal coordination : bond 0.01322 ( 7) metal coordination : angle 2.14237 ( 3) covalent geometry : bond 0.00309 (18658) covalent geometry : angle 0.60860 (25324) *********************** 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 322 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8101 (mp) REVERT: A 458 GLU cc_start: 0.8039 (pp20) cc_final: 0.7615 (pp20) REVERT: A 569 MET cc_start: 0.8844 (mmm) cc_final: 0.8407 (mmm) REVERT: A 796 GLU cc_start: 0.7921 (pm20) cc_final: 0.7651 (pm20) REVERT: B 19 PHE cc_start: 0.7104 (t80) cc_final: 0.6791 (t80) REVERT: B 63 PHE cc_start: 0.6587 (p90) cc_final: 0.6305 (p90) REVERT: B 317 ASP cc_start: 0.7865 (t0) cc_final: 0.6705 (t0) REVERT: B 409 MET cc_start: 0.8790 (tpt) cc_final: 0.8281 (tpt) REVERT: B 424 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 486 MET cc_start: 0.8063 (mmm) cc_final: 0.7757 (mmm) REVERT: C 347 MET cc_start: 0.6685 (tmm) cc_final: 0.6131 (tmm) REVERT: C 350 MET cc_start: 0.8034 (mmm) cc_final: 0.7756 (mmm) REVERT: C 382 MET cc_start: 0.7523 (mtm) cc_final: 0.7179 (mpp) REVERT: C 442 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7035 (mt-10) REVERT: D 92 ILE cc_start: 0.8307 (mm) cc_final: 0.8039 (mt) REVERT: D 173 LEU cc_start: 0.9382 (tp) cc_final: 0.9102 (mm) REVERT: D 379 PHE cc_start: 0.7839 (m-80) cc_final: 0.7550 (m-80) REVERT: D 415 PHE cc_start: 0.8666 (m-80) cc_final: 0.8109 (m-80) REVERT: D 710 MET cc_start: 0.7494 (ttp) cc_final: 0.6848 (tmm) REVERT: D 881 ASP cc_start: 0.8175 (m-30) cc_final: 0.7553 (t0) outliers start: 53 outliers final: 30 residues processed: 304 average time/residue: 0.2743 time to fit residues: 132.9360 Evaluate side-chains 262 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 140 LEU 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 443 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain B residue 32 MET 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 288 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 145 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 252 LEU 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 646 LEU Chi-restraints excluded: chain D residue 911 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 79 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 169 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 0.0070 chunk 74 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 197 GLN D 221 GLN D 230 HIS D 274 ASN D 381 HIS ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 871 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124345 restraints weight = 31808.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122201 restraints weight = 20414.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123843 restraints weight = 17050.840| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 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 = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2012 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= 0.112 Angle : 0.589 10.786 25327 Z= 0.288 Chirality : 0.042 0.334 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.339 21.412 2479 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.61 % Allowed : 16.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2290 helix: 0.13 (0.15), residues: 1179 sheet: -1.50 (0.37), residues: 210 loop : -1.95 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.008 0.001 HIS A 61 PHE 0.017 0.001 PHE C 221 TYR 0.017 0.001 TYR C 278 ARG 0.005 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 641) hydrogen bonds : angle 4.09784 ( 1923) metal coordination : bond 0.01353 ( 7) metal coordination : angle 1.49365 ( 3) covalent geometry : bond 0.00256 (18658) covalent geometry : angle 0.58861 (25324) *********************** 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 326 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 2.251 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 57 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: A 458 GLU cc_start: 0.7881 (pp20) cc_final: 0.7478 (pp20) REVERT: A 569 MET cc_start: 0.8746 (mmm) cc_final: 0.8367 (mmm) REVERT: B 63 PHE cc_start: 0.6705 (p90) cc_final: 0.6421 (p90) REVERT: B 225 TRP cc_start: 0.8544 (m100) cc_final: 0.8301 (m100) REVERT: B 317 ASP cc_start: 0.7821 (t0) cc_final: 0.6777 (t0) REVERT: B 409 MET cc_start: 0.8765 (tpt) cc_final: 0.8287 (tpt) REVERT: B 424 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 486 MET cc_start: 0.8031 (mmm) cc_final: 0.7762 (mmm) REVERT: B 500 ARG cc_start: 0.7393 (mpp80) cc_final: 0.7117 (mpt-90) REVERT: C 163 MET cc_start: 0.6025 (mtt) cc_final: 0.5609 (mmt) REVERT: C 167 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7607 (mttm) REVERT: C 231 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5627 (ptt90) REVERT: C 347 MET cc_start: 0.6792 (tmm) cc_final: 0.6326 (tmm) REVERT: C 350 MET cc_start: 0.8080 (mmm) cc_final: 0.7758 (mmm) REVERT: C 361 HIS cc_start: 0.7189 (t-90) cc_final: 0.6766 (t70) REVERT: C 382 MET cc_start: 0.7362 (mtm) cc_final: 0.6984 (mpp) REVERT: C 442 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6993 (mt-10) REVERT: D 92 ILE cc_start: 0.8300 (mm) cc_final: 0.8071 (mt) REVERT: D 169 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7613 (tppt) REVERT: D 173 LEU cc_start: 0.9316 (tp) cc_final: 0.9086 (mm) REVERT: D 379 PHE cc_start: 0.8005 (m-80) cc_final: 0.7697 (m-80) REVERT: D 415 PHE cc_start: 0.8693 (m-80) cc_final: 0.8123 (m-80) REVERT: D 710 MET cc_start: 0.7468 (ttp) cc_final: 0.6802 (tmm) REVERT: D 881 ASP cc_start: 0.8088 (m-30) cc_final: 0.7613 (t0) outliers start: 53 outliers final: 26 residues processed: 306 average time/residue: 0.2732 time to fit residues: 133.4508 Evaluate side-chains 264 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 139 PHE 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 624 HIS Chi-restraints excluded: chain B residue 32 MET 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 453 ASN 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 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 274 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 190 optimal weight: 0.0000 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4133 r_free = 0.4133 target = 0.167347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123992 restraints weight = 31844.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122568 restraints weight = 21202.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123973 restraints weight = 16867.771| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18665 Z= 0.115 Angle : 0.587 11.607 25327 Z= 0.285 Chirality : 0.043 0.353 2934 Planarity : 0.004 0.057 3236 Dihedral : 4.210 20.344 2479 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.27 % Allowed : 18.28 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2290 helix: 0.34 (0.16), residues: 1175 sheet: -1.26 (0.36), residues: 211 loop : -1.78 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 156 HIS 0.009 0.001 HIS A 61 PHE 0.023 0.001 PHE C 221 TYR 0.016 0.001 TYR C 278 ARG 0.005 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 641) hydrogen bonds : angle 3.97123 ( 1923) metal coordination : bond 0.01247 ( 7) metal coordination : angle 1.55436 ( 3) covalent geometry : bond 0.00267 (18658) covalent geometry : angle 0.58682 (25324) *********************** 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 304 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.086 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: 0.8850 (mt) cc_final: 0.8450 (mt) REVERT: A 458 GLU cc_start: 0.7693 (pp20) cc_final: 0.7403 (pp20) REVERT: A 569 MET cc_start: 0.8721 (mmm) cc_final: 0.8372 (mmm) REVERT: B 63 PHE cc_start: 0.6742 (p90) cc_final: 0.6468 (p90) REVERT: B 225 TRP cc_start: 0.8614 (m100) cc_final: 0.8404 (m100) REVERT: B 317 ASP cc_start: 0.7860 (t0) cc_final: 0.6787 (t0) REVERT: B 409 MET cc_start: 0.8740 (tpt) cc_final: 0.8163 (tpt) REVERT: B 424 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 486 MET cc_start: 0.8040 (mmm) cc_final: 0.7787 (mmm) REVERT: B 500 ARG cc_start: 0.7437 (mpp80) cc_final: 0.7148 (mpt-90) REVERT: C 151 LYS cc_start: 0.7132 (ttpp) cc_final: 0.6770 (ttpp) REVERT: C 163 MET cc_start: 0.6393 (mtt) cc_final: 0.6050 (mmt) REVERT: C 231 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.5503 (ptt90) REVERT: C 337 PHE cc_start: 0.8386 (t80) cc_final: 0.8118 (t80) REVERT: C 347 MET cc_start: 0.6608 (tmm) cc_final: 0.6149 (tmm) REVERT: C 350 MET cc_start: 0.8134 (mmm) cc_final: 0.7824 (mmm) REVERT: C 361 HIS cc_start: 0.7151 (t-90) cc_final: 0.6305 (t-90) REVERT: C 382 MET cc_start: 0.7305 (mtm) cc_final: 0.6951 (mpp) REVERT: C 442 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7057 (mt-10) REVERT: D 169 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7659 (tppt) REVERT: D 173 LEU cc_start: 0.9293 (tp) cc_final: 0.9014 (mm) REVERT: D 379 PHE cc_start: 0.7983 (m-80) cc_final: 0.7632 (m-80) REVERT: D 415 PHE cc_start: 0.8712 (m-80) cc_final: 0.8210 (m-80) REVERT: D 710 MET cc_start: 0.7454 (ttp) cc_final: 0.6686 (tmm) REVERT: D 881 ASP cc_start: 0.8087 (m-30) cc_final: 0.7620 (t0) outliers start: 46 outliers final: 27 residues processed: 289 average time/residue: 0.2669 time to fit residues: 122.9978 Evaluate side-chains 261 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain B residue 32 MET 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 15 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 115 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 168 optimal weight: 0.0570 chunk 103 optimal weight: 0.0170 chunk 169 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 205 optimal weight: 30.0000 chunk 229 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 168 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 = 0.4147 r_free = 0.4147 target = 0.168242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125266 restraints weight = 31865.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123576 restraints weight = 21021.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125508 restraints weight = 16743.602| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2425 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= 0.111 Angle : 0.583 9.688 25327 Z= 0.282 Chirality : 0.042 0.311 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.104 19.849 2479 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.17 % Allowed : 19.21 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2290 helix: 0.43 (0.16), residues: 1179 sheet: -1.12 (0.37), residues: 213 loop : -1.58 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.009 0.001 HIS A 61 PHE 0.017 0.001 PHE C 221 TYR 0.011 0.001 TYR C 179 ARG 0.005 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 641) hydrogen bonds : angle 3.89829 ( 1923) metal coordination : bond 0.01055 ( 7) metal coordination : angle 1.55107 ( 3) covalent geometry : bond 0.00259 (18658) covalent geometry : angle 0.58304 (25324) *********************** 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 295 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: A 140 LEU cc_start: 0.8998 (mt) cc_final: 0.8610 (mt) REVERT: A 458 GLU cc_start: 0.7646 (pp20) cc_final: 0.7380 (pp20) REVERT: A 569 MET cc_start: 0.8725 (mmm) cc_final: 0.8405 (mmm) REVERT: B 63 PHE cc_start: 0.6697 (p90) cc_final: 0.6430 (p90) REVERT: B 157 LYS cc_start: 0.7463 (mmtp) cc_final: 0.7099 (mmtm) REVERT: B 225 TRP cc_start: 0.8717 (m100) cc_final: 0.8508 (m100) REVERT: B 317 ASP cc_start: 0.7911 (t0) cc_final: 0.6965 (t0) REVERT: B 339 PHE cc_start: 0.6118 (m-10) cc_final: 0.5874 (m-10) REVERT: B 409 MET cc_start: 0.8737 (tpt) cc_final: 0.8097 (tpt) REVERT: B 424 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 486 MET cc_start: 0.8050 (mmm) cc_final: 0.7814 (mmm) REVERT: B 500 ARG cc_start: 0.7446 (mpp80) cc_final: 0.7164 (mpt-90) REVERT: C 163 MET cc_start: 0.6452 (mtt) cc_final: 0.6221 (mmt) REVERT: C 337 PHE cc_start: 0.8331 (t80) cc_final: 0.7996 (t80) REVERT: C 347 MET cc_start: 0.6614 (tmm) cc_final: 0.6154 (tmm) REVERT: C 350 MET cc_start: 0.8132 (mmm) cc_final: 0.7803 (mmm) REVERT: C 361 HIS cc_start: 0.7095 (t-90) cc_final: 0.6270 (t-90) REVERT: C 382 MET cc_start: 0.7254 (mtm) cc_final: 0.6943 (mpp) REVERT: C 442 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7035 (mt-10) REVERT: D 169 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7846 (tppt) REVERT: D 173 LEU cc_start: 0.9307 (tp) cc_final: 0.9029 (mm) REVERT: D 379 PHE cc_start: 0.8036 (m-80) cc_final: 0.7778 (m-80) REVERT: D 415 PHE cc_start: 0.8743 (m-80) cc_final: 0.8224 (m-80) REVERT: D 710 MET cc_start: 0.7425 (ttp) cc_final: 0.6689 (tmm) REVERT: D 881 ASP cc_start: 0.8074 (m-30) cc_final: 0.7563 (t0) outliers start: 44 outliers final: 33 residues processed: 283 average time/residue: 0.2632 time to fit residues: 120.1179 Evaluate side-chains 267 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 74 SER 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 624 HIS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 32 MET 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 269 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 490 ILE 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 133 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 240 PHE Chi-restraints excluded: chain C residue 252 LEU 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 227 optimal weight: 6.9990 chunk 103 optimal weight: 0.0270 chunk 85 optimal weight: 0.0010 chunk 117 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 overall best weight: 1.7848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4122 r_free = 0.4122 target = 0.166022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122495 restraints weight = 31905.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121830 restraints weight = 21546.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122514 restraints weight = 18761.385| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18665 Z= 0.160 Angle : 0.631 16.503 25327 Z= 0.302 Chirality : 0.043 0.212 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.206 19.701 2479 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.17 % Allowed : 20.10 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2290 helix: 0.44 (0.16), residues: 1177 sheet: -1.22 (0.36), residues: 214 loop : -1.54 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 35 HIS 0.011 0.001 HIS A 61 PHE 0.018 0.001 PHE C 221 TYR 0.018 0.001 TYR C 179 ARG 0.004 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 641) hydrogen bonds : angle 4.01258 ( 1923) metal coordination : bond 0.01006 ( 7) metal coordination : angle 2.47847 ( 3) covalent geometry : bond 0.00378 (18658) covalent geometry : angle 0.63026 (25324) *********************** 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 290 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8953 (mt) cc_final: 0.8568 (mt) REVERT: A 458 GLU cc_start: 0.7729 (pp20) cc_final: 0.7425 (pp20) REVERT: A 569 MET cc_start: 0.8771 (mmm) cc_final: 0.8414 (mmm) REVERT: B 63 PHE cc_start: 0.6695 (p90) cc_final: 0.6468 (p90) REVERT: B 157 LYS cc_start: 0.7551 (mmtp) cc_final: 0.7321 (mmtp) REVERT: B 225 TRP cc_start: 0.8830 (m100) cc_final: 0.8606 (m100) REVERT: B 317 ASP cc_start: 0.7910 (t0) cc_final: 0.6839 (t0) REVERT: B 409 MET cc_start: 0.8790 (tpt) cc_final: 0.8104 (tpt) REVERT: B 424 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 486 MET cc_start: 0.8052 (mmm) cc_final: 0.7825 (mmm) REVERT: B 500 ARG cc_start: 0.7463 (mpp80) cc_final: 0.7200 (mpt-90) REVERT: C 231 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.5385 (ptt90) REVERT: C 337 PHE cc_start: 0.8421 (t80) cc_final: 0.8208 (t80) REVERT: C 347 MET cc_start: 0.6706 (tmm) cc_final: 0.6217 (tmm) REVERT: C 350 MET cc_start: 0.8100 (mmm) cc_final: 0.7787 (mmm) REVERT: C 361 HIS cc_start: 0.7173 (t-90) cc_final: 0.6359 (t-90) REVERT: C 382 MET cc_start: 0.7320 (mtm) cc_final: 0.7017 (mpp) REVERT: C 442 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7098 (mt-10) REVERT: D 169 LYS cc_start: 0.8359 (mmtp) cc_final: 0.7808 (tppt) REVERT: D 173 LEU cc_start: 0.9314 (tp) cc_final: 0.8939 (mm) REVERT: D 379 PHE cc_start: 0.8045 (m-80) cc_final: 0.7812 (m-80) REVERT: D 387 MET cc_start: 0.7002 (tpp) cc_final: 0.6637 (tmm) REVERT: D 415 PHE cc_start: 0.8733 (m-80) cc_final: 0.8256 (m-80) REVERT: D 710 MET cc_start: 0.7456 (ttp) cc_final: 0.6703 (tmm) REVERT: D 881 ASP cc_start: 0.8074 (m-30) cc_final: 0.7435 (t0) outliers start: 44 outliers final: 35 residues processed: 276 average time/residue: 0.2809 time to fit residues: 122.8090 Evaluate side-chains 266 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 152 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 624 HIS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 32 MET 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 269 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 490 ILE 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 112 VAL Chi-restraints excluded: chain C residue 133 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 C residue 240 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 265 ILE 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 14 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 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** ** 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 = 0.4131 r_free = 0.4131 target = 0.166744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123290 restraints weight = 31898.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121777 restraints weight = 21423.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123401 restraints weight = 17525.719| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2603 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 : 0.617 13.113 25327 Z= 0.295 Chirality : 0.043 0.239 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.151 19.356 2479 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.27 % Allowed : 20.49 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2290 helix: 0.49 (0.16), residues: 1177 sheet: -1.16 (0.36), residues: 214 loop : -1.48 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 35 HIS 0.013 0.001 HIS A 61 PHE 0.025 0.001 PHE C 221 TYR 0.013 0.001 TYR C 353 ARG 0.004 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 641) hydrogen bonds : angle 3.98079 ( 1923) metal coordination : bond 0.00799 ( 7) metal coordination : angle 2.53470 ( 3) covalent geometry : bond 0.00325 (18658) covalent geometry : angle 0.61631 (25324) *********************** 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 293 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8957 (mt) cc_final: 0.8571 (mt) REVERT: A 458 GLU cc_start: 0.7678 (pp20) cc_final: 0.7386 (pp20) REVERT: A 531 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: A 569 MET cc_start: 0.8732 (mmm) cc_final: 0.8371 (mmm) REVERT: B 63 PHE cc_start: 0.6693 (p90) cc_final: 0.6459 (p90) REVERT: B 157 LYS cc_start: 0.7580 (mmtp) cc_final: 0.7377 (mmtp) REVERT: B 225 TRP cc_start: 0.8817 (m100) cc_final: 0.8590 (m100) REVERT: B 317 ASP cc_start: 0.7871 (t0) cc_final: 0.6796 (t0) REVERT: B 409 MET cc_start: 0.8768 (tpt) cc_final: 0.8067 (tpt) REVERT: B 424 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 486 MET cc_start: 0.8026 (mmm) cc_final: 0.7808 (mmm) REVERT: B 500 ARG cc_start: 0.7383 (mpp80) cc_final: 0.7144 (mpt-90) REVERT: C 231 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5283 (ptt90) REVERT: C 337 PHE cc_start: 0.8375 (t80) cc_final: 0.8110 (t80) REVERT: C 347 MET cc_start: 0.6682 (tmm) cc_final: 0.6195 (tmm) REVERT: C 350 MET cc_start: 0.8135 (mmm) cc_final: 0.7795 (mmm) REVERT: C 361 HIS cc_start: 0.7184 (t-90) cc_final: 0.6355 (t-90) REVERT: C 382 MET cc_start: 0.7310 (mtm) cc_final: 0.7025 (mpp) REVERT: C 442 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 169 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7879 (tppt) REVERT: D 173 LEU cc_start: 0.9310 (tp) cc_final: 0.8923 (mm) REVERT: D 379 PHE cc_start: 0.8050 (m-80) cc_final: 0.7805 (m-80) REVERT: D 415 PHE cc_start: 0.8733 (m-80) cc_final: 0.8329 (m-80) REVERT: D 561 MET cc_start: 0.1106 (mtm) cc_final: -0.0445 (mmm) REVERT: D 710 MET cc_start: 0.7438 (ttp) cc_final: 0.6686 (tmm) REVERT: D 881 ASP cc_start: 0.8051 (m-30) cc_final: 0.7431 (t0) outliers start: 46 outliers final: 38 residues processed: 282 average time/residue: 0.2706 time to fit residues: 122.1979 Evaluate side-chains 275 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 32 MET 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 212 THR Chi-restraints excluded: chain B residue 231 TYR 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 397 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 490 ILE 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 112 VAL Chi-restraints excluded: chain C residue 133 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 C residue 240 PHE Chi-restraints excluded: chain C residue 252 LEU 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 837 PHE 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 85 optimal weight: 0.0670 chunk 218 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 67 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 153 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 231 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 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 = 0.4166 r_free = 0.4166 target = 0.170034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127166 restraints weight = 31971.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125581 restraints weight = 23106.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127310 restraints weight = 19829.387| |-----------------------------------------------------------------------------| 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 = 0.83 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 = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2869 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= 0.105 Angle : 0.611 12.583 25327 Z= 0.290 Chirality : 0.042 0.265 2934 Planarity : 0.004 0.061 3236 Dihedral : 3.955 19.432 2479 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.17 % Allowed : 20.74 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2290 helix: 0.59 (0.16), residues: 1178 sheet: -0.97 (0.38), residues: 201 loop : -1.35 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 35 HIS 0.013 0.001 HIS A 61 PHE 0.024 0.001 PHE C 221 TYR 0.015 0.001 TYR D 388 ARG 0.014 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 641) hydrogen bonds : angle 3.89630 ( 1923) metal coordination : bond 0.01017 ( 7) metal coordination : angle 2.43868 ( 3) covalent geometry : bond 0.00237 (18658) covalent geometry : angle 0.61067 (25324) *********************** 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 312 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 2.130 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 140 LEU cc_start: 0.8914 (mt) cc_final: 0.8587 (mt) REVERT: A 458 GLU cc_start: 0.7530 (pp20) cc_final: 0.7196 (pp20) REVERT: A 569 MET cc_start: 0.8704 (mmm) cc_final: 0.8351 (mmm) REVERT: B 63 PHE cc_start: 0.6734 (p90) cc_final: 0.6516 (p90) REVERT: B 317 ASP cc_start: 0.7922 (t0) cc_final: 0.6980 (t0) REVERT: B 409 MET cc_start: 0.8777 (tpt) cc_final: 0.8067 (tpt) REVERT: B 486 MET cc_start: 0.8007 (mmm) cc_final: 0.7776 (mmm) REVERT: B 500 ARG cc_start: 0.7318 (mpp80) cc_final: 0.7101 (mpt-90) REVERT: C 337 PHE cc_start: 0.8391 (t80) cc_final: 0.7952 (t80) REVERT: C 347 MET cc_start: 0.6616 (tmm) cc_final: 0.6260 (tmm) REVERT: C 350 MET cc_start: 0.8039 (mmm) cc_final: 0.7698 (mmm) REVERT: C 355 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7912 (p) REVERT: C 361 HIS cc_start: 0.7035 (t-90) cc_final: 0.6224 (t-90) REVERT: C 382 MET cc_start: 0.7180 (mtm) cc_final: 0.6670 (mpp) REVERT: C 399 MET cc_start: 0.8437 (mmm) cc_final: 0.8183 (mmt) REVERT: C 420 MET cc_start: 0.6024 (mtt) cc_final: 0.5641 (mtm) REVERT: C 442 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7084 (mt-10) REVERT: D 169 LYS cc_start: 0.8357 (mmtp) cc_final: 0.7840 (tppt) REVERT: D 173 LEU cc_start: 0.9306 (tp) cc_final: 0.8911 (mm) REVERT: D 379 PHE cc_start: 0.8095 (m-80) cc_final: 0.7825 (m-80) REVERT: D 415 PHE cc_start: 0.8714 (m-80) cc_final: 0.8341 (m-80) REVERT: D 561 MET cc_start: 0.0976 (mtm) cc_final: -0.0457 (mmm) REVERT: D 710 MET cc_start: 0.7383 (ttp) cc_final: 0.6646 (tmm) REVERT: D 881 ASP cc_start: 0.7940 (m-30) cc_final: 0.7297 (t0) outliers start: 44 outliers final: 34 residues processed: 298 average time/residue: 0.2555 time to fit residues: 123.0285 Evaluate side-chains 279 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 32 MET 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 212 THR Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 397 HIS 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 112 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 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 355 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 187 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 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 = 0.4142 r_free = 0.4142 target = 0.168145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124876 restraints weight = 32071.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123118 restraints weight = 21394.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124727 restraints weight = 17405.871| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- 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 = 0.86 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 = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18665 Z= 0.130 Angle : 0.636 12.836 25327 Z= 0.302 Chirality : 0.043 0.278 2934 Planarity : 0.004 0.060 3236 Dihedral : 3.976 18.187 2479 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.02 % Allowed : 21.28 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2290 helix: 0.62 (0.16), residues: 1179 sheet: -0.95 (0.38), residues: 201 loop : -1.32 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 35 HIS 0.015 0.001 HIS A 61 PHE 0.024 0.001 PHE C 221 TYR 0.029 0.001 TYR C 353 ARG 0.004 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 641) hydrogen bonds : angle 3.91118 ( 1923) metal coordination : bond 0.00906 ( 7) metal coordination : angle 2.44888 ( 3) covalent geometry : bond 0.00306 (18658) covalent geometry : angle 0.63581 (25324) ********************** 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 282 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 1.915 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 140 LEU cc_start: 0.8934 (mt) cc_final: 0.8604 (mt) REVERT: A 218 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 458 GLU cc_start: 0.7616 (pp20) cc_final: 0.7291 (pp20) REVERT: A 569 MET cc_start: 0.8685 (mmm) cc_final: 0.8375 (mmm) REVERT: B 63 PHE cc_start: 0.6761 (p90) cc_final: 0.6529 (p90) REVERT: B 317 ASP cc_start: 0.7927 (t0) cc_final: 0.6989 (t0) REVERT: B 500 ARG cc_start: 0.7402 (mpp80) cc_final: 0.7150 (mpt-90) REVERT: C 163 MET cc_start: 0.5887 (mmt) cc_final: 0.5463 (mmm) REVERT: C 337 PHE cc_start: 0.8325 (t80) cc_final: 0.8106 (t80) REVERT: C 347 MET cc_start: 0.6674 (tmm) cc_final: 0.6294 (tmm) REVERT: C 350 MET cc_start: 0.8037 (mmm) cc_final: 0.7684 (mmm) REVERT: C 355 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 361 HIS cc_start: 0.7033 (t-90) cc_final: 0.6212 (t-90) REVERT: C 382 MET cc_start: 0.7229 (mtm) cc_final: 0.6701 (mpp) REVERT: C 399 MET cc_start: 0.8422 (mmm) cc_final: 0.8179 (mmt) REVERT: C 420 MET cc_start: 0.6093 (mtt) cc_final: 0.5771 (mtm) REVERT: C 442 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7116 (mt-10) REVERT: D 169 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7901 (tppt) REVERT: D 173 LEU cc_start: 0.9314 (tp) cc_final: 0.8931 (mm) REVERT: D 326 MET cc_start: 0.2012 (ppp) cc_final: -0.0344 (mtt) REVERT: D 379 PHE cc_start: 0.8135 (m-80) cc_final: 0.7872 (m-80) REVERT: D 415 PHE cc_start: 0.8688 (m-80) cc_final: 0.8329 (m-80) REVERT: D 561 MET cc_start: 0.0993 (mtm) cc_final: -0.0442 (mmm) REVERT: D 710 MET cc_start: 0.7413 (ttp) cc_final: 0.6654 (tmm) REVERT: D 881 ASP cc_start: 0.7966 (m-30) cc_final: 0.7375 (t0) outliers start: 41 outliers final: 33 residues processed: 269 average time/residue: 0.2630 time to fit residues: 114.5431 Evaluate side-chains 270 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 TRP 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 513 CYS Chi-restraints excluded: chain A residue 724 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 212 THR Chi-restraints excluded: chain B residue 231 TYR 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 397 HIS 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 112 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 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 355 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 17 optimal weight: 0.0980 chunk 149 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 162 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 HIS ** 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 = 0.4154 r_free = 0.4154 target = 0.168992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125949 restraints weight = 31991.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124565 restraints weight = 23465.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125692 restraints weight = 21240.893| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18665 Z= 0.114 Angle : 0.638 12.876 25327 Z= 0.300 Chirality : 0.043 0.314 2934 Planarity : 0.004 0.061 3236 Dihedral : 3.938 19.645 2479 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.97 % Allowed : 21.33 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2290 helix: 0.67 (0.16), residues: 1175 sheet: -0.91 (0.39), residues: 201 loop : -1.26 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 35 HIS 0.014 0.001 HIS A 61 PHE 0.023 0.001 PHE C 221 TYR 0.025 0.001 TYR C 353 ARG 0.004 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 641) hydrogen bonds : angle 3.92863 ( 1923) metal coordination : bond 0.00823 ( 7) metal coordination : angle 2.26850 ( 3) covalent geometry : bond 0.00268 (18658) covalent geometry : angle 0.63744 (25324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5693.76 seconds wall clock time: 99 minutes 52.81 seconds (5992.81 seconds total)