Starting phenix.real_space_refine on Wed Aug 7 01:06:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_18839.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_18839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_18839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_18839.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r2d_18839/08_2024/8r2d_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 Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D GLU 703": "OE1" <-> "OE2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D GLU 905": "OE1" <-> "OE2" Residue "D GLU 943": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 9.99, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.33 Conformation dependent library (CDL) restraints added in 3.2 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: 1.49 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: 4.26 Time building geometry restraints manager: 8.09 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: 99.24 - 106.20: 613 106.20 - 113.16: 10301 113.16 - 120.12: 6676 120.12 - 127.07: 7499 127.07 - 134.03: 235 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: 1.170 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: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 49.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- 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 : 0.004 0.050 18658 Z= 0.273 Angle : 0.705 7.489 25324 Z= 0.404 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.901 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: 0.3144 time to fit residues: 157.2103 Evaluate side-chains 241 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 18658 Z= 0.450 Angle : 0.747 9.363 25324 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 *********************** 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 fitting. rotamer outliers: 47 poor density : 272 time to evaluate : 2.058 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: 0.9355 (tp) cc_final: 0.9014 (tp) REVERT: A 83 PHE cc_start: 0.8126 (m-80) cc_final: 0.7808 (m-80) REVERT: A 458 GLU cc_start: 0.8115 (pp20) cc_final: 0.7885 (pp20) REVERT: B 19 PHE cc_start: 0.7269 (t80) cc_final: 0.6947 (t80) REVERT: B 63 PHE cc_start: 0.6677 (p90) cc_final: 0.6415 (p90) REVERT: B 317 ASP cc_start: 0.7916 (t0) cc_final: 0.6751 (t0) REVERT: B 409 MET cc_start: 0.8661 (tpt) cc_final: 0.8123 (tpt) REVERT: B 430 LEU cc_start: 0.7946 (mt) cc_final: 0.7681 (tp) REVERT: B 486 MET cc_start: 0.8067 (mmm) cc_final: 0.7713 (mmm) REVERT: C 86 TYR cc_start: 0.9202 (t80) cc_final: 0.8932 (t80) REVERT: C 106 ASP cc_start: 0.8844 (t0) cc_final: 0.8185 (t0) REVERT: C 113 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 148 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7969 (mp) REVERT: C 347 MET cc_start: 0.6689 (tmm) cc_final: 0.6349 (tmm) REVERT: C 350 MET cc_start: 0.7985 (mmm) cc_final: 0.7764 (mmm) REVERT: C 382 MET cc_start: 0.7742 (mtm) cc_final: 0.7361 (mpp) REVERT: C 442 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7190 (mt-10) REVERT: D 173 LEU cc_start: 0.9338 (tp) cc_final: 0.9056 (mm) REVERT: D 379 PHE cc_start: 0.7690 (m-80) cc_final: 0.7175 (m-80) REVERT: D 415 PHE cc_start: 0.8692 (m-80) cc_final: 0.8139 (m-80) REVERT: D 725 MET cc_start: 0.8260 (mmm) cc_final: 0.8038 (mmm) outliers start: 47 outliers final: 28 residues processed: 298 average time/residue: 0.2785 time to fit residues: 129.1832 Evaluate side-chains 260 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 148 LEU 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 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18658 Z= 0.193 Angle : 0.603 8.730 25324 Z= 0.298 Chirality : 0.043 0.214 2934 Planarity : 0.005 0.059 3236 Dihedral : 4.572 21.619 2479 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.41 % Allowed : 15.86 % Favored : 81.72 % 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: -1.72 (0.18), residues: 2290 helix: -0.16 (0.15), residues: 1183 sheet: -1.77 (0.37), residues: 208 loop : -2.26 (0.20), residues: 899 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 0.018 0.001 TYR C 278 ARG 0.005 0.000 ARG C 196 *********************** 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 321 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 2.047 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: 0.8246 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 458 GLU cc_start: 0.7907 (pp20) cc_final: 0.7491 (pp20) REVERT: A 569 MET cc_start: 0.8821 (mmm) cc_final: 0.8431 (mmm) REVERT: A 796 GLU cc_start: 0.7884 (pm20) cc_final: 0.7683 (pm20) REVERT: B 63 PHE cc_start: 0.6556 (p90) cc_final: 0.6292 (p90) REVERT: B 317 ASP cc_start: 0.7711 (t0) cc_final: 0.6574 (t0) REVERT: B 409 MET cc_start: 0.8680 (tpt) cc_final: 0.8214 (tpt) REVERT: B 486 MET cc_start: 0.7961 (mmm) cc_final: 0.7657 (mmm) REVERT: B 500 ARG cc_start: 0.7389 (mpp80) cc_final: 0.7105 (mpt-90) REVERT: C 148 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7657 (mp) REVERT: C 347 MET cc_start: 0.6760 (tmm) cc_final: 0.6309 (tmm) REVERT: C 350 MET cc_start: 0.8025 (mmm) cc_final: 0.7761 (mmm) REVERT: C 382 MET cc_start: 0.7474 (mtm) cc_final: 0.7137 (mpp) REVERT: C 442 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7002 (mt-10) REVERT: D 92 ILE cc_start: 0.8331 (mm) cc_final: 0.8067 (mt) REVERT: D 173 LEU cc_start: 0.9337 (tp) cc_final: 0.9063 (mm) REVERT: D 379 PHE cc_start: 0.7681 (m-80) cc_final: 0.7454 (m-80) REVERT: D 415 PHE cc_start: 0.8572 (m-80) cc_final: 0.8040 (m-80) REVERT: D 881 ASP cc_start: 0.8070 (m-30) cc_final: 0.7572 (t0) outliers start: 49 outliers final: 26 residues processed: 304 average time/residue: 0.2640 time to fit residues: 127.6049 Evaluate side-chains 262 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 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 453 ASN Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 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 208 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 100 optimal weight: 0.5980 chunk 141 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18658 Z= 0.169 Angle : 0.592 10.605 25324 Z= 0.289 Chirality : 0.043 0.324 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.328 21.426 2479 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.76 % Allowed : 16.80 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.18), residues: 2290 helix: 0.17 (0.15), residues: 1179 sheet: -1.36 (0.38), residues: 196 loop : -1.95 (0.21), residues: 915 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 0.007 0.000 ARG A 785 *********************** 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 328 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 2.039 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: 0.8902 (mt) cc_final: 0.8545 (mt) REVERT: A 218 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 443 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: A 458 GLU cc_start: 0.7806 (pp20) cc_final: 0.7392 (pp20) REVERT: A 569 MET cc_start: 0.8748 (mmm) cc_final: 0.8407 (mmm) REVERT: B 63 PHE cc_start: 0.6668 (p90) cc_final: 0.6408 (p90) REVERT: B 225 TRP cc_start: 0.8520 (m100) cc_final: 0.8280 (m100) REVERT: B 317 ASP cc_start: 0.7774 (t0) cc_final: 0.6723 (t0) REVERT: B 409 MET cc_start: 0.8700 (tpt) cc_final: 0.8213 (tpt) REVERT: B 486 MET cc_start: 0.7967 (mmm) cc_final: 0.7706 (mmm) REVERT: B 500 ARG cc_start: 0.7363 (mpp80) cc_final: 0.7084 (mpt-90) REVERT: C 113 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: C 163 MET cc_start: 0.6224 (mtt) cc_final: 0.5412 (mmt) REVERT: C 231 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5574 (ptt90) REVERT: C 347 MET cc_start: 0.6812 (tmm) cc_final: 0.6350 (tmm) REVERT: C 350 MET cc_start: 0.8058 (mmm) cc_final: 0.7751 (mmm) REVERT: C 361 HIS cc_start: 0.7162 (t-90) cc_final: 0.6762 (t70) REVERT: C 382 MET cc_start: 0.7340 (mtm) cc_final: 0.6964 (mpp) REVERT: C 387 MET cc_start: 0.7781 (mmm) cc_final: 0.7573 (mmm) REVERT: C 442 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6956 (mt-10) REVERT: D 92 ILE cc_start: 0.8292 (mm) cc_final: 0.8087 (mt) REVERT: D 169 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7624 (tppt) REVERT: D 173 LEU cc_start: 0.9266 (tp) cc_final: 0.9043 (mm) REVERT: D 379 PHE cc_start: 0.7782 (m-80) cc_final: 0.7548 (m-80) REVERT: D 415 PHE cc_start: 0.8577 (m-80) cc_final: 0.8068 (m-80) REVERT: D 710 MET cc_start: 0.7514 (tmm) cc_final: 0.6870 (tmm) REVERT: D 881 ASP cc_start: 0.8002 (m-30) cc_final: 0.7555 (t0) outliers start: 56 outliers final: 27 residues processed: 307 average time/residue: 0.2785 time to fit residues: 136.0834 Evaluate side-chains 262 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 443 GLN 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 453 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 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 186 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18658 Z= 0.189 Angle : 0.587 8.254 25324 Z= 0.287 Chirality : 0.043 0.292 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.241 20.537 2479 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.32 % Allowed : 18.18 % Favored : 79.51 % 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: -0.99 (0.18), residues: 2290 helix: 0.33 (0.16), residues: 1174 sheet: -1.29 (0.36), residues: 212 loop : -1.77 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 156 HIS 0.009 0.001 HIS A 61 PHE 0.020 0.001 PHE C 221 TYR 0.017 0.001 TYR C 278 ARG 0.005 0.000 ARG C 231 *********************** 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 299 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8945 (mt) cc_final: 0.8577 (mt) REVERT: A 218 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 458 GLU cc_start: 0.7631 (pp20) cc_final: 0.7328 (pp20) REVERT: A 569 MET cc_start: 0.8717 (mmm) cc_final: 0.8400 (mmm) REVERT: B 63 PHE cc_start: 0.6712 (p90) cc_final: 0.6462 (p90) REVERT: B 225 TRP cc_start: 0.8602 (m100) cc_final: 0.8379 (m100) REVERT: B 317 ASP cc_start: 0.7775 (t0) cc_final: 0.6715 (t0) REVERT: B 409 MET cc_start: 0.8705 (tpt) cc_final: 0.8144 (tpt) REVERT: B 486 MET cc_start: 0.7978 (mmm) cc_final: 0.7727 (mmm) REVERT: B 500 ARG cc_start: 0.7264 (mpp80) cc_final: 0.7019 (mpt-90) REVERT: C 163 MET cc_start: 0.6422 (mtt) cc_final: 0.6118 (mmt) REVERT: C 230 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6326 (mt-10) REVERT: C 231 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5464 (ptt90) REVERT: C 347 MET cc_start: 0.6647 (tmm) cc_final: 0.6205 (tmm) REVERT: C 350 MET cc_start: 0.8127 (mmm) cc_final: 0.7820 (mmm) REVERT: C 361 HIS cc_start: 0.7144 (t-90) cc_final: 0.6316 (t-90) REVERT: C 382 MET cc_start: 0.7294 (mtm) cc_final: 0.6933 (mpp) REVERT: C 387 MET cc_start: 0.7690 (mmm) cc_final: 0.7465 (mmm) REVERT: C 442 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7024 (mt-10) REVERT: D 92 ILE cc_start: 0.8285 (mm) cc_final: 0.8053 (mt) REVERT: D 169 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7667 (tppt) REVERT: D 173 LEU cc_start: 0.9260 (tp) cc_final: 0.8982 (mm) REVERT: D 379 PHE cc_start: 0.7812 (m-80) cc_final: 0.7520 (m-80) REVERT: D 389 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: D 415 PHE cc_start: 0.8608 (m-80) cc_final: 0.8168 (m-80) REVERT: D 710 MET cc_start: 0.7493 (tmm) cc_final: 0.6864 (tmm) REVERT: D 881 ASP cc_start: 0.7983 (m-30) cc_final: 0.7494 (t0) outliers start: 47 outliers final: 29 residues processed: 283 average time/residue: 0.3312 time to fit residues: 151.6863 Evaluate side-chains 261 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 443 GLN 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 269 ILE Chi-restraints excluded: chain B residue 304 VAL 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 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 289 HIS 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 75 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 224 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18658 Z= 0.172 Angle : 0.587 12.161 25324 Z= 0.283 Chirality : 0.043 0.323 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.128 19.865 2479 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.17 % Allowed : 19.31 % Favored : 78.52 % 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: -0.80 (0.18), residues: 2290 helix: 0.40 (0.16), residues: 1179 sheet: -1.12 (0.36), residues: 213 loop : -1.59 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 35 HIS 0.010 0.001 HIS A 61 PHE 0.020 0.001 PHE C 221 TYR 0.012 0.001 TYR C 179 ARG 0.005 0.000 ARG C 231 *********************** 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 fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8964 (mt) cc_final: 0.8629 (mt) REVERT: A 218 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8008 (mm) REVERT: A 458 GLU cc_start: 0.7569 (pp20) cc_final: 0.7244 (pp20) REVERT: A 569 MET cc_start: 0.8728 (mmm) cc_final: 0.8432 (mmm) REVERT: A 796 GLU cc_start: 0.7523 (pm20) cc_final: 0.7234 (pm20) REVERT: B 63 PHE cc_start: 0.6670 (p90) cc_final: 0.6424 (p90) REVERT: B 157 LYS cc_start: 0.7399 (mmtp) cc_final: 0.7015 (mmtm) REVERT: B 225 TRP cc_start: 0.8685 (m100) cc_final: 0.8478 (m100) REVERT: B 317 ASP cc_start: 0.7849 (t0) cc_final: 0.6896 (t0) REVERT: B 339 PHE cc_start: 0.6097 (m-10) cc_final: 0.5859 (m-10) REVERT: B 409 MET cc_start: 0.8679 (tpt) cc_final: 0.8059 (tpt) REVERT: B 424 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 486 MET cc_start: 0.7963 (mmm) cc_final: 0.7728 (mmm) REVERT: B 500 ARG cc_start: 0.7346 (mpp80) cc_final: 0.7110 (mpt-90) REVERT: C 163 MET cc_start: 0.6437 (mtt) cc_final: 0.6227 (mmt) REVERT: C 337 PHE cc_start: 0.8302 (t80) cc_final: 0.8014 (t80) REVERT: C 347 MET cc_start: 0.6653 (tmm) cc_final: 0.6200 (tmm) REVERT: C 350 MET cc_start: 0.8113 (mmm) cc_final: 0.7799 (mmm) REVERT: C 361 HIS cc_start: 0.7074 (t-90) cc_final: 0.6298 (t-90) REVERT: C 382 MET cc_start: 0.7234 (mtm) cc_final: 0.6912 (mpp) REVERT: C 387 MET cc_start: 0.7638 (mmm) cc_final: 0.7428 (mmm) REVERT: C 442 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6995 (mt-10) REVERT: D 169 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7868 (tppt) REVERT: D 173 LEU cc_start: 0.9272 (tp) cc_final: 0.8992 (mm) REVERT: D 415 PHE cc_start: 0.8635 (m-80) cc_final: 0.8185 (m-80) REVERT: D 561 MET cc_start: 0.1315 (mtm) cc_final: -0.0241 (mmm) REVERT: D 707 MET cc_start: 0.6369 (ttt) cc_final: 0.5817 (ptm) REVERT: D 710 MET cc_start: 0.7482 (tmm) cc_final: 0.6853 (tmm) REVERT: D 725 MET cc_start: 0.8133 (mmm) cc_final: 0.7900 (mpp) REVERT: D 881 ASP cc_start: 0.7952 (m-30) cc_final: 0.7474 (t0) outliers start: 44 outliers final: 32 residues processed: 282 average time/residue: 0.2712 time to fit residues: 122.2132 Evaluate side-chains 270 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain B residue 11 THR 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 231 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP 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 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 289 HIS 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 216 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 188 optimal weight: 0.0050 chunk 125 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18658 Z= 0.181 Angle : 0.606 17.003 25324 Z= 0.287 Chirality : 0.042 0.316 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.055 19.190 2479 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 19.85 % Favored : 78.03 % 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: -0.67 (0.18), residues: 2290 helix: 0.47 (0.16), residues: 1180 sheet: -1.06 (0.37), residues: 213 loop : -1.45 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 35 HIS 0.012 0.001 HIS A 61 PHE 0.019 0.001 PHE A 36 TYR 0.015 0.001 TYR B 236 ARG 0.003 0.000 ARG A 785 *********************** 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 293 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8927 (mt) cc_final: 0.8598 (mt) REVERT: A 218 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7988 (mm) REVERT: A 458 GLU cc_start: 0.7621 (pp20) cc_final: 0.7280 (pp20) REVERT: A 569 MET cc_start: 0.8722 (mmm) cc_final: 0.8425 (mmm) REVERT: B 63 PHE cc_start: 0.6636 (p90) cc_final: 0.6433 (p90) REVERT: B 225 TRP cc_start: 0.8720 (m100) cc_final: 0.8502 (m100) REVERT: B 317 ASP cc_start: 0.7865 (t0) cc_final: 0.6824 (t0) REVERT: B 409 MET cc_start: 0.8678 (tpt) cc_final: 0.8017 (tpt) REVERT: B 486 MET cc_start: 0.7962 (mmm) cc_final: 0.7750 (mmm) REVERT: B 500 ARG cc_start: 0.7355 (mpp80) cc_final: 0.7151 (mpt-90) REVERT: C 337 PHE cc_start: 0.8251 (t80) cc_final: 0.7934 (t80) REVERT: C 347 MET cc_start: 0.6667 (tmm) cc_final: 0.6210 (tmm) REVERT: C 350 MET cc_start: 0.8057 (mmm) cc_final: 0.7741 (mmm) REVERT: C 361 HIS cc_start: 0.7087 (t-90) cc_final: 0.6330 (t-90) REVERT: C 382 MET cc_start: 0.7221 (mtm) cc_final: 0.6908 (mpp) REVERT: C 442 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7029 (mt-10) REVERT: D 169 LYS cc_start: 0.8393 (mmtp) cc_final: 0.7859 (tppt) REVERT: D 173 LEU cc_start: 0.9279 (tp) cc_final: 0.8896 (mm) REVERT: D 387 MET cc_start: 0.6833 (tpp) cc_final: 0.6465 (tmm) REVERT: D 415 PHE cc_start: 0.8638 (m-80) cc_final: 0.8221 (m-80) REVERT: D 561 MET cc_start: 0.1087 (mtm) cc_final: -0.0401 (mmm) REVERT: D 710 MET cc_start: 0.7439 (tmm) cc_final: 0.7031 (tmm) REVERT: D 881 ASP cc_start: 0.7891 (m-30) cc_final: 0.7288 (t0) outliers start: 43 outliers final: 34 residues processed: 281 average time/residue: 0.2609 time to fit residues: 117.6989 Evaluate side-chains 272 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 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 231 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP 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 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 289 HIS 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 89 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18658 Z= 0.195 Angle : 0.610 14.473 25324 Z= 0.291 Chirality : 0.043 0.375 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.061 19.079 2479 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.22 % Allowed : 20.30 % Favored : 77.49 % 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: -0.58 (0.18), residues: 2290 helix: 0.52 (0.16), residues: 1178 sheet: -0.99 (0.37), residues: 213 loop : -1.39 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 35 HIS 0.012 0.001 HIS A 61 PHE 0.026 0.001 PHE C 221 TYR 0.013 0.001 TYR C 353 ARG 0.004 0.000 ARG C 338 *********************** 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 295 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 250 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8938 (mt) cc_final: 0.8618 (mt) REVERT: A 218 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 458 GLU cc_start: 0.7610 (pp20) cc_final: 0.7254 (pp20) REVERT: A 569 MET cc_start: 0.8734 (mmm) cc_final: 0.8424 (mmm) REVERT: B 63 PHE cc_start: 0.6724 (p90) cc_final: 0.6523 (p90) REVERT: B 157 LYS cc_start: 0.7491 (mmtp) cc_final: 0.7222 (mmtm) REVERT: B 199 TYR cc_start: 0.7715 (m-80) cc_final: 0.7372 (m-80) REVERT: B 225 TRP cc_start: 0.8697 (m100) cc_final: 0.8488 (m100) REVERT: B 317 ASP cc_start: 0.7866 (t0) cc_final: 0.6819 (t0) REVERT: B 409 MET cc_start: 0.8683 (tpt) cc_final: 0.7996 (tpt) REVERT: B 486 MET cc_start: 0.7966 (mmm) cc_final: 0.7757 (mmm) REVERT: C 231 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.5271 (ptt90) REVERT: C 337 PHE cc_start: 0.8369 (t80) cc_final: 0.8070 (t80) REVERT: C 347 MET cc_start: 0.6694 (tmm) cc_final: 0.6226 (tmm) REVERT: C 350 MET cc_start: 0.8046 (mmm) cc_final: 0.7721 (mmm) REVERT: C 361 HIS cc_start: 0.7100 (t-90) cc_final: 0.6349 (t-90) REVERT: C 382 MET cc_start: 0.7212 (mtm) cc_final: 0.6920 (mpp) REVERT: C 442 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7005 (mt-10) REVERT: D 169 LYS cc_start: 0.8399 (mmtp) cc_final: 0.7890 (tppt) REVERT: D 173 LEU cc_start: 0.9279 (tp) cc_final: 0.8886 (mm) REVERT: D 415 PHE cc_start: 0.8620 (m-80) cc_final: 0.8256 (m-80) REVERT: D 561 MET cc_start: 0.1098 (mtm) cc_final: -0.0386 (mmm) REVERT: D 707 MET cc_start: 0.6411 (ttt) cc_final: 0.5846 (ptm) REVERT: D 710 MET cc_start: 0.7474 (tmm) cc_final: 0.7094 (tmm) outliers start: 45 outliers final: 36 residues processed: 282 average time/residue: 0.2612 time to fit residues: 117.2718 Evaluate side-chains 270 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 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 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 231 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP 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 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 289 HIS Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 848 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 956 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.1980 chunk 208 optimal weight: 10.0000 chunk 214 optimal weight: 40.0000 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 C 332 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18658 Z= 0.234 Angle : 0.631 10.710 25324 Z= 0.302 Chirality : 0.044 0.312 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.131 19.326 2479 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.12 % Allowed : 20.64 % 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: -0.59 (0.18), residues: 2290 helix: 0.48 (0.16), residues: 1180 sheet: -1.00 (0.37), residues: 213 loop : -1.35 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 35 HIS 0.013 0.001 HIS A 61 PHE 0.025 0.001 PHE C 221 TYR 0.024 0.001 TYR C 353 ARG 0.005 0.000 ARG C 258 *********************** 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 286 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8922 (mt) cc_final: 0.8599 (mt) REVERT: B 63 PHE cc_start: 0.6749 (p90) cc_final: 0.6536 (p90) REVERT: B 108 MET cc_start: 0.8149 (mmm) cc_final: 0.7881 (tpp) REVERT: B 157 LYS cc_start: 0.7576 (mmtp) cc_final: 0.7032 (mmtm) REVERT: B 199 TYR cc_start: 0.7685 (m-80) cc_final: 0.7305 (m-80) REVERT: B 225 TRP cc_start: 0.8825 (m100) cc_final: 0.8580 (m100) REVERT: B 317 ASP cc_start: 0.7924 (t0) cc_final: 0.6958 (t0) REVERT: C 181 MET cc_start: 0.6970 (mmm) cc_final: 0.6750 (mmm) REVERT: C 231 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5274 (ptt90) REVERT: C 347 MET cc_start: 0.6750 (tmm) cc_final: 0.6382 (tmm) REVERT: C 350 MET cc_start: 0.8016 (mmm) cc_final: 0.7692 (mmm) REVERT: C 361 HIS cc_start: 0.7108 (t-90) cc_final: 0.6303 (t-90) REVERT: C 382 MET cc_start: 0.7237 (mtm) cc_final: 0.6933 (mpp) REVERT: C 442 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7052 (mt-10) REVERT: D 169 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7852 (tppt) REVERT: D 173 LEU cc_start: 0.9289 (tp) cc_final: 0.8894 (mm) REVERT: D 400 MET cc_start: 0.7720 (tpp) cc_final: 0.7450 (tpp) REVERT: D 415 PHE cc_start: 0.8599 (m-80) cc_final: 0.8258 (m-80) REVERT: D 561 MET cc_start: 0.1105 (mtm) cc_final: -0.0374 (mmm) outliers start: 43 outliers final: 38 residues processed: 273 average time/residue: 0.2600 time to fit residues: 114.7646 Evaluate side-chains 272 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 152 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 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 231 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 ASP 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 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 289 HIS 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 220 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 0.0570 chunk 146 optimal weight: 0.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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** B 210 GLN C 94 HIS C 332 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18658 Z= 0.272 Angle : 0.670 11.576 25324 Z= 0.320 Chirality : 0.045 0.269 2934 Planarity : 0.004 0.058 3236 Dihedral : 4.259 21.264 2479 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.22 % Allowed : 20.79 % Favored : 77.00 % 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: -0.64 (0.18), residues: 2290 helix: 0.47 (0.16), residues: 1177 sheet: -1.11 (0.37), residues: 214 loop : -1.38 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 35 HIS 0.016 0.001 HIS A 61 PHE 0.034 0.002 PHE D 379 TYR 0.024 0.001 TYR C 353 ARG 0.008 0.000 ARG A 785 ********************** 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 279 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8903 (mt) cc_final: 0.8626 (mt) REVERT: A 458 GLU cc_start: 0.7759 (pp20) cc_final: 0.7111 (pp20) REVERT: A 569 MET cc_start: 0.8809 (mmm) cc_final: 0.8470 (mmm) REVERT: B 63 PHE cc_start: 0.6762 (p90) cc_final: 0.6527 (p90) REVERT: B 157 LYS cc_start: 0.7644 (mmtp) cc_final: 0.7078 (mmtm) REVERT: B 199 TYR cc_start: 0.7543 (m-80) cc_final: 0.7292 (m-80) REVERT: B 225 TRP cc_start: 0.8848 (m100) cc_final: 0.8589 (m100) REVERT: B 317 ASP cc_start: 0.7861 (t0) cc_final: 0.6724 (t0) REVERT: C 163 MET cc_start: 0.6773 (mmt) cc_final: 0.6084 (mmt) REVERT: C 231 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5294 (ptt90) REVERT: C 321 VAL cc_start: 0.8755 (t) cc_final: 0.8535 (m) REVERT: C 347 MET cc_start: 0.6776 (tmm) cc_final: 0.6396 (tmm) REVERT: C 350 MET cc_start: 0.7964 (mmm) cc_final: 0.7633 (mmm) REVERT: C 361 HIS cc_start: 0.7149 (t-90) cc_final: 0.6317 (t-90) REVERT: C 382 MET cc_start: 0.7283 (mtm) cc_final: 0.6999 (mpp) REVERT: C 399 MET cc_start: 0.8353 (mmm) cc_final: 0.8082 (mmt) REVERT: C 442 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7091 (mt-10) REVERT: D 169 LYS cc_start: 0.8450 (mmtp) cc_final: 0.7861 (tppt) REVERT: D 173 LEU cc_start: 0.9302 (tp) cc_final: 0.8889 (mm) REVERT: D 415 PHE cc_start: 0.8557 (m-80) cc_final: 0.8209 (m-80) REVERT: D 561 MET cc_start: 0.1127 (mtm) cc_final: -0.0359 (mmm) outliers start: 45 outliers final: 39 residues processed: 266 average time/residue: 0.2565 time to fit residues: 111.4416 Evaluate side-chains 269 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 513 CYS 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 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 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 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 289 HIS Chi-restraints excluded: chain D residue 581 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 77 optimal weight: 0.0670 chunk 189 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 161 optimal weight: 0.0370 overall best weight: 1.6200 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122597 restraints weight = 32021.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121407 restraints weight = 21681.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122625 restraints weight = 17653.240| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 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 = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18658 Z= 0.239 Angle : 0.660 12.325 25324 Z= 0.313 Chirality : 0.044 0.277 2934 Planarity : 0.004 0.059 3236 Dihedral : 4.236 19.552 2479 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.17 % Allowed : 21.28 % Favored : 76.55 % 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: -0.65 (0.18), residues: 2290 helix: 0.49 (0.16), residues: 1181 sheet: -1.26 (0.37), residues: 207 loop : -1.40 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 35 HIS 0.014 0.001 HIS A 61 PHE 0.030 0.001 PHE D 379 TYR 0.023 0.001 TYR C 353 ARG 0.008 0.000 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.14 seconds wall clock time: 62 minutes 38.34 seconds (3758.34 seconds total)