Starting phenix.real_space_refine on Wed Mar 4 09:31:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kup_9579/03_2026/6kup_9579.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 P 23 5.49 5 S 109 5.16 5 C 7703 2.51 5 N 2092 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12254 At special positions: 0 Unit cell: (111.52, 110.16, 110.16, 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) S 109 16.00 P 23 15.00 O 2327 8.00 N 2092 7.00 C 7703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 513.2 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 48.0% alpha, 7.7% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.743A pdb=" N ALA A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.720A pdb=" N THR A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.100A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.749A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.049A pdb=" N ASP A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.136A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.591A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.799A pdb=" N CYS A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.700A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.796A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.997A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.618A pdb=" N GLU B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.645A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.534A pdb=" N CYS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.772A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.873A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 4.042A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.549A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.677A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.646A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 560 removed outlier: 3.512A pdb=" N ALA B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.831A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.577A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.573A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.989A pdb=" N LEU B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.739A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 30 through 37 removed outlier: 3.964A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.553A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.529A pdb=" N THR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.730A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.601A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.674A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.863A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.604A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.830A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.724A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 478 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.561A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA9, first strand: chain 'B' and resid 438 through 443 removed outlier: 4.133A pdb=" N PHE B 448 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.723A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 512 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.44 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: 3691 1.34 - 1.46: 2351 1.46 - 1.58: 6278 1.58 - 1.70: 44 1.70 - 1.82: 181 Bond restraints: 12545 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.27e-02 6.20e+03 2.11e+01 bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.371 -0.037 8.40e-03 1.42e+04 1.98e+01 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.25e-02 6.40e+03 6.81e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.428 0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" C LEU A 203 " pdb=" N PRO A 204 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 ... (remaining 12540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16147 1.65 - 3.30: 669 3.30 - 4.95: 109 4.95 - 6.60: 23 6.60 - 8.25: 14 Bond angle restraints: 16962 Sorted by residual: angle pdb=" C LEU B 540 " pdb=" N SER B 541 " pdb=" CA SER B 541 " ideal model delta sigma weight residual 120.51 127.61 -7.10 1.45e+00 4.76e-01 2.40e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.69 -5.12 1.25e+00 6.40e-01 1.68e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" N ILE C 159 " pdb=" CA ILE C 159 " pdb=" C ILE C 159 " ideal model delta sigma weight residual 111.62 108.63 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" C TRP A 357 " pdb=" N GLN A 358 " pdb=" CA GLN A 358 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 ... (remaining 16957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 7253 15.20 - 30.40: 309 30.40 - 45.60: 102 45.60 - 60.80: 29 60.80 - 76.01: 27 Dihedral angle restraints: 7720 sinusoidal: 3460 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR B 328 " pdb=" C THR B 328 " pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1412 0.054 - 0.109: 369 0.109 - 0.163: 65 0.163 - 0.217: 6 0.217 - 0.272: 3 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 231 " pdb=" CA ILE C 231 " pdb=" CG1 ILE C 231 " pdb=" CG2 ILE C 231 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 155 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO C 156 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 342 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 343 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 731 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C ILE B 731 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE B 731 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1933 2.76 - 3.30: 11010 3.30 - 3.83: 19001 3.83 - 4.37: 22663 4.37 - 4.90: 38410 Nonbonded interactions: 93017 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.227 3.120 nonbonded pdb=" O LEU B 324 " pdb=" OG1 THR B 328 " model vdw 2.296 3.040 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.297 3.040 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.308 3.040 nonbonded pdb=" O VAL B 341 " pdb=" OG1 THR B 344 " model vdw 2.313 3.040 ... (remaining 93012 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 0.058 12545 Z= 0.206 Angle : 0.809 8.248 16962 Z= 0.452 Chirality : 0.050 0.272 1855 Planarity : 0.006 0.069 2070 Dihedral : 11.438 76.006 4954 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.16), residues: 1441 helix: -3.42 (0.12), residues: 647 sheet: -1.84 (0.52), residues: 91 loop : -3.28 (0.19), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.018 0.002 TYR A 549 PHE 0.026 0.002 PHE B 726 TRP 0.029 0.003 TRP A 386 HIS 0.007 0.002 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00409 (12545) covalent geometry : angle 0.80867 (16962) hydrogen bonds : bond 0.14526 ( 531) hydrogen bonds : angle 9.05112 ( 1457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 566 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 TRP cc_start: 0.7767 (t-100) cc_final: 0.7098 (t-100) REVERT: A 278 ASP cc_start: 0.8685 (t0) cc_final: 0.8424 (t0) REVERT: A 288 LEU cc_start: 0.9683 (tp) cc_final: 0.9462 (tt) REVERT: A 332 GLU cc_start: 0.7990 (tt0) cc_final: 0.7661 (pt0) REVERT: A 364 GLU cc_start: 0.8341 (mp0) cc_final: 0.8053 (mp0) REVERT: A 382 PHE cc_start: 0.7765 (t80) cc_final: 0.7121 (t80) REVERT: A 386 TRP cc_start: 0.8882 (t-100) cc_final: 0.8255 (t-100) REVERT: A 453 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7673 (tp30) REVERT: A 495 ASP cc_start: 0.8666 (m-30) cc_final: 0.8178 (m-30) REVERT: A 498 TYR cc_start: 0.8407 (p90) cc_final: 0.8098 (p90) REVERT: A 547 PHE cc_start: 0.9005 (m-80) cc_final: 0.8558 (m-10) REVERT: A 555 MET cc_start: 0.8238 (mmm) cc_final: 0.7761 (mmm) REVERT: A 562 TRP cc_start: 0.7924 (m100) cc_final: 0.7212 (m100) REVERT: A 578 GLU cc_start: 0.8803 (tt0) cc_final: 0.8426 (tt0) REVERT: A 600 LYS cc_start: 0.9278 (tppt) cc_final: 0.8776 (tptp) REVERT: A 601 ARG cc_start: 0.8753 (mmt180) cc_final: 0.8530 (mmm160) REVERT: A 639 ASP cc_start: 0.7436 (m-30) cc_final: 0.6535 (m-30) REVERT: A 650 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8329 (mtmt) REVERT: A 661 ASP cc_start: 0.7648 (t0) cc_final: 0.7440 (t0) REVERT: A 684 ASN cc_start: 0.9318 (t0) cc_final: 0.9101 (t0) REVERT: B 10 LEU cc_start: 0.9528 (mt) cc_final: 0.9275 (tt) REVERT: B 45 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8004 (ttp-170) REVERT: B 52 THR cc_start: 0.8465 (t) cc_final: 0.8184 (t) REVERT: B 85 VAL cc_start: 0.9349 (t) cc_final: 0.8882 (t) REVERT: B 147 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8247 (mm-40) REVERT: B 151 ASP cc_start: 0.8473 (t0) cc_final: 0.7641 (t70) REVERT: B 155 GLU cc_start: 0.7725 (tt0) cc_final: 0.7412 (pt0) REVERT: B 182 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7681 (mtmm) REVERT: B 234 GLU cc_start: 0.7109 (tt0) cc_final: 0.6432 (pm20) REVERT: B 237 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8283 (mptt) REVERT: B 255 LYS cc_start: 0.8564 (tptt) cc_final: 0.8185 (tptt) REVERT: B 311 TRP cc_start: 0.9365 (t-100) cc_final: 0.9085 (t-100) REVERT: B 336 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8430 (mmtp) REVERT: B 389 LEU cc_start: 0.9390 (mt) cc_final: 0.9165 (tp) REVERT: B 410 MET cc_start: 0.5922 (mtp) cc_final: 0.5689 (mtt) REVERT: B 541 SER cc_start: 0.8831 (p) cc_final: 0.8034 (p) REVERT: B 576 ILE cc_start: 0.9376 (mt) cc_final: 0.8945 (tp) REVERT: B 578 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7006 (ptm-80) REVERT: B 610 GLU cc_start: 0.8754 (mp0) cc_final: 0.7888 (pm20) REVERT: B 612 LEU cc_start: 0.8521 (tp) cc_final: 0.7930 (tp) REVERT: B 627 ASN cc_start: 0.8756 (t0) cc_final: 0.8426 (t0) REVERT: B 689 CYS cc_start: 0.8548 (m) cc_final: 0.8255 (m) REVERT: B 736 TYR cc_start: 0.8102 (t80) cc_final: 0.6476 (t80) REVERT: C 55 MET cc_start: 0.8368 (mmm) cc_final: 0.8089 (mmm) REVERT: C 85 LYS cc_start: 0.5817 (mmtm) cc_final: 0.4828 (ptpt) REVERT: C 96 LEU cc_start: 0.8227 (mt) cc_final: 0.7923 (mt) REVERT: C 102 ILE cc_start: 0.8970 (mt) cc_final: 0.8580 (mm) REVERT: C 213 MET cc_start: 0.8486 (ptm) cc_final: 0.8167 (ppp) REVERT: C 218 PHE cc_start: 0.7928 (m-10) cc_final: 0.6824 (m-80) REVERT: C 247 TRP cc_start: 0.8394 (p-90) cc_final: 0.7656 (p90) outliers start: 2 outliers final: 0 residues processed: 566 average time/residue: 0.1389 time to fit residues: 107.2100 Evaluate side-chains 357 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 277 HIS A 560 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 640 ASN B 70 ASN B 147 GLN B 477 ASN B 667 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109216 restraints weight = 27057.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112525 restraints weight = 15344.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114807 restraints weight = 10097.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116298 restraints weight = 7396.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117412 restraints weight = 5944.410| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12545 Z= 0.146 Angle : 0.645 12.969 16962 Z= 0.333 Chirality : 0.042 0.163 1855 Planarity : 0.005 0.055 2070 Dihedral : 11.604 74.408 1924 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.20), residues: 1441 helix: -0.97 (0.18), residues: 654 sheet: -1.63 (0.54), residues: 96 loop : -2.87 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 212 TYR 0.038 0.002 TYR B 736 PHE 0.027 0.002 PHE B 108 TRP 0.022 0.002 TRP A 386 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00317 (12545) covalent geometry : angle 0.64500 (16962) hydrogen bonds : bond 0.04875 ( 531) hydrogen bonds : angle 5.20755 ( 1457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7914 (mp0) cc_final: 0.7711 (pp20) REVERT: A 271 TRP cc_start: 0.7479 (t-100) cc_final: 0.6992 (t-100) REVERT: A 315 TYR cc_start: 0.8163 (m-80) cc_final: 0.7775 (m-80) REVERT: A 386 TRP cc_start: 0.8892 (t-100) cc_final: 0.7809 (t-100) REVERT: A 390 MET cc_start: 0.8638 (ptm) cc_final: 0.8105 (ttm) REVERT: A 453 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7509 (tp30) REVERT: A 547 PHE cc_start: 0.8893 (m-80) cc_final: 0.8232 (m-10) REVERT: A 558 LEU cc_start: 0.8857 (tt) cc_final: 0.8620 (tt) REVERT: A 568 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.8253 (ptt-90) REVERT: A 643 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7467 (mm-30) REVERT: A 650 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8355 (ptpt) REVERT: A 654 MET cc_start: 0.8739 (tpp) cc_final: 0.8208 (tpp) REVERT: A 684 ASN cc_start: 0.9228 (t0) cc_final: 0.8934 (t0) REVERT: B 2 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7106 (mt-10) REVERT: B 52 THR cc_start: 0.8415 (t) cc_final: 0.8160 (t) REVERT: B 85 VAL cc_start: 0.9189 (t) cc_final: 0.8983 (t) REVERT: B 90 MET cc_start: 0.9156 (ptm) cc_final: 0.8593 (ptm) REVERT: B 92 SER cc_start: 0.9244 (m) cc_final: 0.8993 (p) REVERT: B 112 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8242 (mp0) REVERT: B 133 ASP cc_start: 0.8211 (t70) cc_final: 0.7754 (m-30) REVERT: B 151 ASP cc_start: 0.8548 (t0) cc_final: 0.7869 (t70) REVERT: B 174 GLU cc_start: 0.8661 (tt0) cc_final: 0.7937 (tt0) REVERT: B 234 GLU cc_start: 0.7086 (tt0) cc_final: 0.6615 (pm20) REVERT: B 237 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8449 (mptt) REVERT: B 250 ILE cc_start: 0.8765 (mt) cc_final: 0.8483 (mp) REVERT: B 255 LYS cc_start: 0.8793 (tptt) cc_final: 0.8404 (tptt) REVERT: B 270 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7059 (mp0) REVERT: B 312 ASN cc_start: 0.8990 (m-40) cc_final: 0.8387 (m-40) REVERT: B 408 MET cc_start: 0.6853 (ttm) cc_final: 0.6200 (ttp) REVERT: B 453 ILE cc_start: 0.9134 (pt) cc_final: 0.8819 (tp) REVERT: B 460 MET cc_start: 0.8520 (tpp) cc_final: 0.8143 (tpp) REVERT: B 461 GLU cc_start: 0.8149 (pt0) cc_final: 0.7856 (pt0) REVERT: B 490 LEU cc_start: 0.9025 (tp) cc_final: 0.8645 (tp) REVERT: B 492 GLU cc_start: 0.8093 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 528 MET cc_start: 0.8905 (mtm) cc_final: 0.8492 (mtp) REVERT: B 560 TYR cc_start: 0.8623 (m-10) cc_final: 0.8380 (m-10) REVERT: B 574 MET cc_start: 0.8281 (mmm) cc_final: 0.8076 (tpp) REVERT: B 578 ARG cc_start: 0.7844 (tpp80) cc_final: 0.6924 (ptm-80) REVERT: B 587 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7912 (mmmt) REVERT: B 591 LEU cc_start: 0.9201 (tp) cc_final: 0.8917 (tp) REVERT: B 681 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7480 (mm-30) REVERT: B 714 ILE cc_start: 0.8787 (mm) cc_final: 0.8573 (mm) REVERT: C 32 TYR cc_start: 0.8263 (t80) cc_final: 0.7553 (t80) REVERT: C 51 MET cc_start: 0.8988 (tpp) cc_final: 0.8683 (tpp) REVERT: C 55 MET cc_start: 0.8429 (mmm) cc_final: 0.8174 (mmm) REVERT: C 85 LYS cc_start: 0.5785 (mmtm) cc_final: 0.5519 (mmmm) REVERT: C 131 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8141 (mtm110) REVERT: C 213 MET cc_start: 0.9179 (ptm) cc_final: 0.8718 (ppp) REVERT: C 214 ILE cc_start: 0.9340 (mt) cc_final: 0.8860 (mt) REVERT: C 218 PHE cc_start: 0.8226 (m-10) cc_final: 0.7065 (m-80) REVERT: C 242 LEU cc_start: 0.8754 (tt) cc_final: 0.8496 (tt) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1300 time to fit residues: 75.8818 Evaluate side-chains 327 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN C 155 GLN C 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104800 restraints weight = 27551.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108024 restraints weight = 15940.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110238 restraints weight = 10674.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111783 restraints weight = 7945.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112873 restraints weight = 6407.348| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12545 Z= 0.169 Angle : 0.629 10.536 16962 Z= 0.325 Chirality : 0.042 0.153 1855 Planarity : 0.005 0.057 2070 Dihedral : 11.466 74.317 1924 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 0.31 % Allowed : 2.33 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.21), residues: 1441 helix: -0.11 (0.19), residues: 664 sheet: -1.49 (0.51), residues: 100 loop : -2.74 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 232 TYR 0.013 0.002 TYR A 205 PHE 0.016 0.001 PHE A 481 TRP 0.016 0.002 TRP A 386 HIS 0.007 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00372 (12545) covalent geometry : angle 0.62852 (16962) hydrogen bonds : bond 0.04713 ( 531) hydrogen bonds : angle 4.78520 ( 1457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 372 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7108 (tpm170) cc_final: 0.6622 (tpm170) REVERT: A 315 TYR cc_start: 0.8278 (m-80) cc_final: 0.8068 (m-80) REVERT: A 332 GLU cc_start: 0.7617 (pt0) cc_final: 0.6641 (pm20) REVERT: A 340 ASP cc_start: 0.8643 (t0) cc_final: 0.8323 (t70) REVERT: A 364 GLU cc_start: 0.8403 (mp0) cc_final: 0.8041 (mp0) REVERT: A 390 MET cc_start: 0.8471 (ptm) cc_final: 0.8240 (ttp) REVERT: A 406 MET cc_start: 0.7628 (tpp) cc_final: 0.6808 (mtt) REVERT: A 428 GLU cc_start: 0.7779 (tp30) cc_final: 0.7097 (tp30) REVERT: A 453 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7500 (tp30) REVERT: A 547 PHE cc_start: 0.8723 (m-80) cc_final: 0.8211 (m-80) REVERT: A 570 LEU cc_start: 0.8384 (mp) cc_final: 0.8146 (mp) REVERT: A 643 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8112 (mp0) REVERT: A 649 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: A 654 MET cc_start: 0.8543 (tpp) cc_final: 0.8175 (tpp) REVERT: A 708 TYR cc_start: 0.8682 (m-80) cc_final: 0.8346 (m-80) REVERT: B 2 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6394 (mp0) REVERT: B 52 THR cc_start: 0.8589 (t) cc_final: 0.8373 (t) REVERT: B 78 LEU cc_start: 0.8809 (tp) cc_final: 0.8293 (tp) REVERT: B 80 LYS cc_start: 0.9341 (mmmm) cc_final: 0.9075 (mmtm) REVERT: B 90 MET cc_start: 0.9192 (ptm) cc_final: 0.8964 (ptm) REVERT: B 92 SER cc_start: 0.9289 (m) cc_final: 0.9029 (p) REVERT: B 133 ASP cc_start: 0.8333 (t70) cc_final: 0.7895 (m-30) REVERT: B 174 GLU cc_start: 0.8705 (tt0) cc_final: 0.7908 (tt0) REVERT: B 183 PHE cc_start: 0.8751 (p90) cc_final: 0.8146 (p90) REVERT: B 221 LYS cc_start: 0.9327 (mtpt) cc_final: 0.9124 (mtmt) REVERT: B 234 GLU cc_start: 0.7080 (tt0) cc_final: 0.6841 (pm20) REVERT: B 237 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8585 (mptt) REVERT: B 255 LYS cc_start: 0.8697 (tptt) cc_final: 0.8276 (tptt) REVERT: B 312 ASN cc_start: 0.8987 (m-40) cc_final: 0.8411 (m-40) REVERT: B 320 TYR cc_start: 0.8431 (m-10) cc_final: 0.8209 (m-10) REVERT: B 328 THR cc_start: 0.8365 (p) cc_final: 0.7982 (t) REVERT: B 349 LYS cc_start: 0.9181 (pttm) cc_final: 0.8742 (ptpp) REVERT: B 375 MET cc_start: 0.8855 (mtp) cc_final: 0.8624 (mtp) REVERT: B 389 LEU cc_start: 0.9197 (tp) cc_final: 0.8953 (tt) REVERT: B 408 MET cc_start: 0.7080 (ttm) cc_final: 0.6790 (ttp) REVERT: B 460 MET cc_start: 0.8504 (tpp) cc_final: 0.8288 (tpp) REVERT: B 461 GLU cc_start: 0.8027 (pt0) cc_final: 0.7818 (pt0) REVERT: B 490 LEU cc_start: 0.9202 (tp) cc_final: 0.8624 (tp) REVERT: B 492 GLU cc_start: 0.8196 (tt0) cc_final: 0.7915 (tm-30) REVERT: B 496 MET cc_start: 0.8759 (mtp) cc_final: 0.8399 (mtt) REVERT: B 547 MET cc_start: 0.9154 (tpp) cc_final: 0.8514 (ttm) REVERT: B 574 MET cc_start: 0.8356 (mmm) cc_final: 0.7945 (tpp) REVERT: B 591 LEU cc_start: 0.9264 (tp) cc_final: 0.9000 (tp) REVERT: B 661 SER cc_start: 0.8968 (m) cc_final: 0.8653 (t) REVERT: B 663 ARG cc_start: 0.6866 (tpp-160) cc_final: 0.6326 (tpp-160) REVERT: B 681 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 708 MET cc_start: 0.7297 (pmm) cc_final: 0.6775 (pmm) REVERT: B 749 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6870 (tm-30) REVERT: C 85 LYS cc_start: 0.5879 (mmtm) cc_final: 0.4669 (ptpt) REVERT: C 102 ILE cc_start: 0.9010 (mt) cc_final: 0.8779 (mp) REVERT: C 103 THR cc_start: 0.9227 (p) cc_final: 0.8908 (t) REVERT: C 160 LYS cc_start: 0.9090 (tttt) cc_final: 0.8862 (tttm) REVERT: C 213 MET cc_start: 0.9186 (ptm) cc_final: 0.8708 (ppp) REVERT: C 218 PHE cc_start: 0.8413 (m-10) cc_final: 0.7301 (m-80) outliers start: 4 outliers final: 1 residues processed: 373 average time/residue: 0.1316 time to fit residues: 69.0240 Evaluate side-chains 316 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.130613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106795 restraints weight = 27463.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110011 restraints weight = 15979.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112257 restraints weight = 10779.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113818 restraints weight = 8041.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114857 restraints weight = 6503.123| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12545 Z= 0.121 Angle : 0.579 10.989 16962 Z= 0.297 Chirality : 0.041 0.173 1855 Planarity : 0.004 0.047 2070 Dihedral : 11.292 73.943 1924 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1441 helix: 0.28 (0.20), residues: 667 sheet: -1.21 (0.52), residues: 105 loop : -2.59 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.013 0.001 TYR B 6 PHE 0.024 0.001 PHE B 108 TRP 0.012 0.001 TRP A 386 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00268 (12545) covalent geometry : angle 0.57916 (16962) hydrogen bonds : bond 0.04081 ( 531) hydrogen bonds : angle 4.51275 ( 1457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.7483 (pt0) cc_final: 0.7010 (pm20) REVERT: A 340 ASP cc_start: 0.8695 (t0) cc_final: 0.8454 (t70) REVERT: A 364 GLU cc_start: 0.8418 (mp0) cc_final: 0.8030 (mp0) REVERT: A 406 MET cc_start: 0.7907 (tpp) cc_final: 0.7486 (mtt) REVERT: A 526 VAL cc_start: 0.9035 (t) cc_final: 0.8793 (t) REVERT: A 547 PHE cc_start: 0.8883 (m-80) cc_final: 0.8344 (m-80) REVERT: A 654 MET cc_start: 0.8522 (tpp) cc_final: 0.8128 (tpp) REVERT: A 684 ASN cc_start: 0.9221 (t0) cc_final: 0.8697 (m110) REVERT: A 708 TYR cc_start: 0.8650 (m-80) cc_final: 0.8288 (m-80) REVERT: B 4 ASN cc_start: 0.9375 (t0) cc_final: 0.8969 (t0) REVERT: B 52 THR cc_start: 0.8495 (t) cc_final: 0.8221 (t) REVERT: B 65 ARG cc_start: 0.7480 (ttm170) cc_final: 0.6654 (ttm-80) REVERT: B 78 LEU cc_start: 0.8676 (tp) cc_final: 0.8176 (tp) REVERT: B 80 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9095 (mmtm) REVERT: B 87 ILE cc_start: 0.9242 (pt) cc_final: 0.9024 (pt) REVERT: B 92 SER cc_start: 0.9337 (m) cc_final: 0.9117 (p) REVERT: B 112 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8323 (mp0) REVERT: B 133 ASP cc_start: 0.8310 (t70) cc_final: 0.7885 (m-30) REVERT: B 155 GLU cc_start: 0.8739 (tt0) cc_final: 0.8205 (pt0) REVERT: B 174 GLU cc_start: 0.8718 (tt0) cc_final: 0.8103 (tt0) REVERT: B 237 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8543 (mptt) REVERT: B 250 ILE cc_start: 0.8661 (mp) cc_final: 0.8420 (mp) REVERT: B 312 ASN cc_start: 0.8855 (m110) cc_final: 0.8262 (m-40) REVERT: B 320 TYR cc_start: 0.8312 (m-10) cc_final: 0.7925 (m-10) REVERT: B 336 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8244 (ptmt) REVERT: B 375 MET cc_start: 0.8634 (mtp) cc_final: 0.8338 (mtp) REVERT: B 383 ASN cc_start: 0.8617 (m-40) cc_final: 0.8227 (m110) REVERT: B 397 MET cc_start: 0.8355 (tpp) cc_final: 0.8131 (tpp) REVERT: B 402 CYS cc_start: 0.8435 (t) cc_final: 0.8137 (t) REVERT: B 408 MET cc_start: 0.7611 (ttm) cc_final: 0.6809 (ttp) REVERT: B 490 LEU cc_start: 0.9054 (tp) cc_final: 0.8537 (tp) REVERT: B 496 MET cc_start: 0.8671 (mtp) cc_final: 0.8420 (mtt) REVERT: B 574 MET cc_start: 0.8286 (mmm) cc_final: 0.7926 (tpp) REVERT: B 587 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7956 (mmmt) REVERT: B 661 SER cc_start: 0.8853 (m) cc_final: 0.8587 (t) REVERT: B 681 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 708 MET cc_start: 0.7359 (pmm) cc_final: 0.6824 (pmm) REVERT: B 749 GLN cc_start: 0.7091 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 10 GLU cc_start: 0.9094 (mp0) cc_final: 0.8595 (mp0) REVERT: C 11 TYR cc_start: 0.8594 (t80) cc_final: 0.8391 (t80) REVERT: C 55 MET cc_start: 0.8421 (mmm) cc_final: 0.8052 (mmm) REVERT: C 81 ASP cc_start: 0.7526 (t0) cc_final: 0.7118 (t0) REVERT: C 85 LYS cc_start: 0.5842 (mmtm) cc_final: 0.5594 (mmmm) REVERT: C 102 ILE cc_start: 0.9137 (mt) cc_final: 0.8921 (mp) REVERT: C 103 THR cc_start: 0.9179 (p) cc_final: 0.8845 (t) REVERT: C 118 ILE cc_start: 0.8729 (mt) cc_final: 0.8484 (mt) REVERT: C 123 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8349 (mmmt) REVERT: C 154 THR cc_start: 0.9006 (p) cc_final: 0.8739 (p) REVERT: C 160 LYS cc_start: 0.9091 (tttt) cc_final: 0.8807 (tttm) REVERT: C 213 MET cc_start: 0.9166 (ptm) cc_final: 0.8792 (ppp) REVERT: C 218 PHE cc_start: 0.8368 (m-10) cc_final: 0.7295 (m-80) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.1218 time to fit residues: 65.1126 Evaluate side-chains 298 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 97 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105423 restraints weight = 27765.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108610 restraints weight = 16250.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110818 restraints weight = 11024.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112317 restraints weight = 8271.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113391 restraints weight = 6712.441| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12545 Z= 0.134 Angle : 0.605 9.959 16962 Z= 0.310 Chirality : 0.041 0.149 1855 Planarity : 0.004 0.080 2070 Dihedral : 11.269 73.878 1924 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.22), residues: 1441 helix: 0.40 (0.20), residues: 673 sheet: -1.24 (0.54), residues: 100 loop : -2.51 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 625 TYR 0.021 0.001 TYR B 6 PHE 0.021 0.001 PHE B 108 TRP 0.016 0.001 TRP C 38 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00300 (12545) covalent geometry : angle 0.60523 (16962) hydrogen bonds : bond 0.04175 ( 531) hydrogen bonds : angle 4.46169 ( 1457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8957 (t80) cc_final: 0.8749 (t80) REVERT: A 275 LYS cc_start: 0.9039 (pttp) cc_final: 0.8419 (pptt) REVERT: A 278 ASP cc_start: 0.8695 (t0) cc_final: 0.8490 (t0) REVERT: A 332 GLU cc_start: 0.7405 (pt0) cc_final: 0.6959 (pm20) REVERT: A 340 ASP cc_start: 0.8730 (t0) cc_final: 0.8433 (t70) REVERT: A 364 GLU cc_start: 0.8301 (mp0) cc_final: 0.7903 (mp0) REVERT: A 442 LYS cc_start: 0.9048 (mttp) cc_final: 0.8603 (mmtp) REVERT: A 453 GLU cc_start: 0.8226 (tp30) cc_final: 0.7929 (tp30) REVERT: A 478 ASP cc_start: 0.9320 (p0) cc_final: 0.7753 (p0) REVERT: A 639 ASP cc_start: 0.7751 (t0) cc_final: 0.7205 (t0) REVERT: A 684 ASN cc_start: 0.9271 (t0) cc_final: 0.8969 (t0) REVERT: A 692 ASP cc_start: 0.8625 (t0) cc_final: 0.8293 (t0) REVERT: A 708 TYR cc_start: 0.8582 (m-80) cc_final: 0.8249 (m-80) REVERT: B 4 ASN cc_start: 0.9500 (t0) cc_final: 0.8846 (t0) REVERT: B 7 LEU cc_start: 0.9587 (mt) cc_final: 0.9318 (mt) REVERT: B 52 THR cc_start: 0.8567 (t) cc_final: 0.8274 (t) REVERT: B 78 LEU cc_start: 0.8731 (tp) cc_final: 0.8477 (tt) REVERT: B 80 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9107 (mmtm) REVERT: B 92 SER cc_start: 0.9331 (m) cc_final: 0.9074 (p) REVERT: B 133 ASP cc_start: 0.8497 (t70) cc_final: 0.7998 (m-30) REVERT: B 155 GLU cc_start: 0.8607 (tt0) cc_final: 0.8245 (pt0) REVERT: B 174 GLU cc_start: 0.8779 (tt0) cc_final: 0.8391 (tm-30) REVERT: B 237 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8546 (mptt) REVERT: B 312 ASN cc_start: 0.8887 (m110) cc_final: 0.8223 (m-40) REVERT: B 320 TYR cc_start: 0.8272 (m-10) cc_final: 0.7818 (m-10) REVERT: B 336 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8211 (mttp) REVERT: B 375 MET cc_start: 0.8733 (mtp) cc_final: 0.8445 (mtp) REVERT: B 383 ASN cc_start: 0.8558 (m-40) cc_final: 0.8353 (m110) REVERT: B 389 LEU cc_start: 0.9148 (tp) cc_final: 0.8837 (tt) REVERT: B 408 MET cc_start: 0.7776 (ttm) cc_final: 0.7028 (ttp) REVERT: B 462 MET cc_start: 0.8440 (mtm) cc_final: 0.8090 (mtp) REVERT: B 490 LEU cc_start: 0.9013 (tp) cc_final: 0.8604 (tp) REVERT: B 496 MET cc_start: 0.8767 (mtp) cc_final: 0.8436 (mtt) REVERT: B 547 MET cc_start: 0.9081 (tpp) cc_final: 0.8363 (ttm) REVERT: B 574 MET cc_start: 0.8242 (mmm) cc_final: 0.7828 (tpp) REVERT: B 587 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8063 (mmmt) REVERT: B 614 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7416 (tt0) REVERT: B 661 SER cc_start: 0.8817 (m) cc_final: 0.8594 (t) REVERT: B 663 ARG cc_start: 0.6917 (tpp-160) cc_final: 0.6172 (tpp80) REVERT: B 681 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 749 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 10 GLU cc_start: 0.8997 (mp0) cc_final: 0.8646 (mp0) REVERT: C 51 MET cc_start: 0.8926 (tpp) cc_final: 0.8651 (tpp) REVERT: C 55 MET cc_start: 0.8493 (mmm) cc_final: 0.8186 (mmm) REVERT: C 81 ASP cc_start: 0.7560 (t0) cc_final: 0.7105 (t0) REVERT: C 85 LYS cc_start: 0.6181 (mmtm) cc_final: 0.5836 (mmmm) REVERT: C 103 THR cc_start: 0.9183 (p) cc_final: 0.8794 (t) REVERT: C 123 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8276 (mmmt) REVERT: C 160 LYS cc_start: 0.9110 (tttt) cc_final: 0.8830 (tttm) REVERT: C 167 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8243 (mppt) REVERT: C 213 MET cc_start: 0.9161 (ptm) cc_final: 0.8765 (ppp) REVERT: C 218 PHE cc_start: 0.8469 (m-10) cc_final: 0.7417 (m-80) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1145 time to fit residues: 60.4137 Evaluate side-chains 301 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105516 restraints weight = 28092.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108509 restraints weight = 16570.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110695 restraints weight = 11302.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112203 restraints weight = 8473.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113239 restraints weight = 6857.671| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12545 Z= 0.128 Angle : 0.596 10.195 16962 Z= 0.305 Chirality : 0.041 0.147 1855 Planarity : 0.005 0.070 2070 Dihedral : 11.226 73.753 1924 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1441 helix: 0.54 (0.21), residues: 669 sheet: -1.17 (0.56), residues: 95 loop : -2.41 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.023 0.001 TYR B 6 PHE 0.021 0.001 PHE B 108 TRP 0.018 0.001 TRP A 381 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00285 (12545) covalent geometry : angle 0.59559 (16962) hydrogen bonds : bond 0.04068 ( 531) hydrogen bonds : angle 4.41089 ( 1457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9011 (t80) cc_final: 0.8693 (t80) REVERT: A 332 GLU cc_start: 0.7409 (pt0) cc_final: 0.6954 (pm20) REVERT: A 340 ASP cc_start: 0.8675 (t0) cc_final: 0.8420 (t70) REVERT: A 364 GLU cc_start: 0.8243 (mp0) cc_final: 0.7872 (mp0) REVERT: A 409 MET cc_start: 0.8623 (mmm) cc_final: 0.8246 (mmm) REVERT: A 442 LYS cc_start: 0.9140 (mttp) cc_final: 0.8669 (mmtm) REVERT: A 627 LEU cc_start: 0.9549 (mt) cc_final: 0.9332 (mp) REVERT: A 639 ASP cc_start: 0.7888 (t0) cc_final: 0.7559 (t0) REVERT: A 684 ASN cc_start: 0.9116 (t0) cc_final: 0.8760 (t0) REVERT: A 692 ASP cc_start: 0.8579 (t0) cc_final: 0.8072 (t0) REVERT: A 693 ARG cc_start: 0.8585 (mmt180) cc_final: 0.8382 (mmt180) REVERT: A 708 TYR cc_start: 0.8475 (m-80) cc_final: 0.8212 (m-80) REVERT: B 2 GLU cc_start: 0.5648 (mp0) cc_final: 0.5136 (mp0) REVERT: B 80 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9070 (mmtm) REVERT: B 85 VAL cc_start: 0.9122 (t) cc_final: 0.8906 (t) REVERT: B 90 MET cc_start: 0.8954 (ptm) cc_final: 0.8630 (ptm) REVERT: B 92 SER cc_start: 0.9312 (m) cc_final: 0.9072 (p) REVERT: B 112 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8324 (mp0) REVERT: B 133 ASP cc_start: 0.8331 (t70) cc_final: 0.7919 (m-30) REVERT: B 138 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7185 (ttp-110) REVERT: B 147 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 155 GLU cc_start: 0.8571 (tt0) cc_final: 0.8317 (pt0) REVERT: B 174 GLU cc_start: 0.8782 (tt0) cc_final: 0.8348 (tm-30) REVERT: B 237 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8769 (mptt) REVERT: B 250 ILE cc_start: 0.8803 (mp) cc_final: 0.8557 (mp) REVERT: B 312 ASN cc_start: 0.8982 (m110) cc_final: 0.8251 (m-40) REVERT: B 320 TYR cc_start: 0.8099 (m-10) cc_final: 0.7733 (m-10) REVERT: B 336 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8341 (mttp) REVERT: B 375 MET cc_start: 0.8713 (mtp) cc_final: 0.8491 (mtp) REVERT: B 402 CYS cc_start: 0.8382 (t) cc_final: 0.8111 (t) REVERT: B 408 MET cc_start: 0.7869 (ttm) cc_final: 0.7348 (ttm) REVERT: B 442 LEU cc_start: 0.8850 (tp) cc_final: 0.8173 (tp) REVERT: B 462 MET cc_start: 0.8428 (mtm) cc_final: 0.8016 (mtp) REVERT: B 496 MET cc_start: 0.8767 (mtp) cc_final: 0.8484 (mtt) REVERT: B 574 MET cc_start: 0.8200 (mmm) cc_final: 0.7814 (tpp) REVERT: B 587 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7924 (mmmt) REVERT: B 663 ARG cc_start: 0.6925 (tpp-160) cc_final: 0.6269 (tpp80) REVERT: B 681 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7444 (mm-30) REVERT: C 10 GLU cc_start: 0.9042 (mp0) cc_final: 0.8707 (mp0) REVERT: C 55 MET cc_start: 0.8259 (mmm) cc_final: 0.8014 (mmm) REVERT: C 81 ASP cc_start: 0.7590 (t0) cc_final: 0.7230 (t0) REVERT: C 85 LYS cc_start: 0.6432 (mmtm) cc_final: 0.6022 (mmmm) REVERT: C 123 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8186 (mmmt) REVERT: C 160 LYS cc_start: 0.9128 (tttt) cc_final: 0.8863 (tttm) REVERT: C 213 MET cc_start: 0.9173 (ptm) cc_final: 0.8782 (ppp) REVERT: C 218 PHE cc_start: 0.8509 (m-10) cc_final: 0.7565 (m-80) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1171 time to fit residues: 59.2052 Evaluate side-chains 287 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 579 GLN B 383 ASN B 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100606 restraints weight = 28317.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103635 restraints weight = 16735.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105681 restraints weight = 11378.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107028 restraints weight = 8597.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108026 restraints weight = 7053.473| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12545 Z= 0.205 Angle : 0.684 8.274 16962 Z= 0.354 Chirality : 0.044 0.163 1855 Planarity : 0.005 0.065 2070 Dihedral : 11.383 74.011 1924 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.61 % Favored : 91.33 % Rotamer: Outliers : 0.08 % Allowed : 1.87 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1441 helix: 0.30 (0.20), residues: 664 sheet: -1.22 (0.53), residues: 98 loop : -2.43 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 629 TYR 0.026 0.002 TYR B 6 PHE 0.035 0.002 PHE A 382 TRP 0.025 0.002 TRP C 53 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00460 (12545) covalent geometry : angle 0.68363 (16962) hydrogen bonds : bond 0.04991 ( 531) hydrogen bonds : angle 4.69152 ( 1457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 HIS cc_start: 0.8692 (m90) cc_final: 0.8480 (m90) REVERT: A 332 GLU cc_start: 0.7283 (pt0) cc_final: 0.6816 (pm20) REVERT: A 340 ASP cc_start: 0.8760 (t0) cc_final: 0.8540 (t70) REVERT: A 364 GLU cc_start: 0.8112 (mp0) cc_final: 0.7484 (mp0) REVERT: A 639 ASP cc_start: 0.8338 (t0) cc_final: 0.8024 (t0) REVERT: A 643 GLU cc_start: 0.8581 (pm20) cc_final: 0.8160 (mp0) REVERT: A 656 LEU cc_start: 0.9521 (tt) cc_final: 0.9310 (tp) REVERT: B 2 GLU cc_start: 0.5356 (mp0) cc_final: 0.5045 (mp0) REVERT: B 78 LEU cc_start: 0.8855 (tp) cc_final: 0.8591 (tt) REVERT: B 80 LYS cc_start: 0.9301 (mmmm) cc_final: 0.9082 (mmtm) REVERT: B 92 SER cc_start: 0.9353 (m) cc_final: 0.9068 (p) REVERT: B 133 ASP cc_start: 0.8392 (t70) cc_final: 0.7760 (m-30) REVERT: B 155 GLU cc_start: 0.8599 (tt0) cc_final: 0.8377 (pt0) REVERT: B 174 GLU cc_start: 0.8885 (tt0) cc_final: 0.8170 (tt0) REVERT: B 219 PHE cc_start: 0.8795 (t80) cc_final: 0.8549 (t80) REVERT: B 237 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8844 (mptt) REVERT: B 312 ASN cc_start: 0.9101 (m110) cc_final: 0.8313 (m-40) REVERT: B 320 TYR cc_start: 0.8343 (m-10) cc_final: 0.7845 (m-10) REVERT: B 408 MET cc_start: 0.8235 (ttm) cc_final: 0.7626 (ttp) REVERT: B 442 LEU cc_start: 0.8861 (tp) cc_final: 0.8328 (tp) REVERT: B 462 MET cc_start: 0.8319 (mtm) cc_final: 0.7925 (mtp) REVERT: B 528 MET cc_start: 0.9158 (mtt) cc_final: 0.8902 (mtt) REVERT: B 547 MET cc_start: 0.8767 (tpp) cc_final: 0.8281 (ttm) REVERT: B 587 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7936 (mmmt) REVERT: B 629 ARG cc_start: 0.7865 (mpp-170) cc_final: 0.7241 (mtm180) REVERT: B 663 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6332 (tpp80) REVERT: B 681 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7678 (mm-30) REVERT: C 32 TYR cc_start: 0.8183 (t80) cc_final: 0.7865 (t80) REVERT: C 51 MET cc_start: 0.8937 (tpp) cc_final: 0.8389 (tpp) REVERT: C 85 LYS cc_start: 0.6424 (mmtm) cc_final: 0.5911 (mmmm) REVERT: C 103 THR cc_start: 0.9266 (p) cc_final: 0.8968 (t) REVERT: C 123 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8313 (mmmt) REVERT: C 155 GLN cc_start: 0.8320 (tp40) cc_final: 0.7921 (tp40) REVERT: C 160 LYS cc_start: 0.9179 (tttt) cc_final: 0.8964 (tttm) REVERT: C 200 TYR cc_start: 0.7008 (m-80) cc_final: 0.6306 (m-80) REVERT: C 213 MET cc_start: 0.9206 (ptm) cc_final: 0.8816 (ptm) REVERT: C 232 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8468 (ttm110) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.1239 time to fit residues: 57.1601 Evaluate side-chains 276 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 116 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104468 restraints weight = 28363.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107468 restraints weight = 16914.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109568 restraints weight = 11584.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111011 restraints weight = 8746.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111970 restraints weight = 7123.679| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12545 Z= 0.121 Angle : 0.622 10.111 16962 Z= 0.314 Chirality : 0.042 0.148 1855 Planarity : 0.004 0.063 2070 Dihedral : 11.218 73.592 1924 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 0.08 % Allowed : 0.70 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.22), residues: 1441 helix: 0.42 (0.20), residues: 665 sheet: -1.06 (0.52), residues: 98 loop : -2.36 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.018 0.001 TYR B 6 PHE 0.018 0.001 PHE A 652 TRP 0.014 0.001 TRP C 38 HIS 0.005 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00274 (12545) covalent geometry : angle 0.62208 (16962) hydrogen bonds : bond 0.04210 ( 531) hydrogen bonds : angle 4.42215 ( 1457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9101 (t80) cc_final: 0.8668 (t80) REVERT: A 332 GLU cc_start: 0.7213 (pt0) cc_final: 0.6668 (pm20) REVERT: A 340 ASP cc_start: 0.8696 (t0) cc_final: 0.8492 (t70) REVERT: A 409 MET cc_start: 0.8623 (mmm) cc_final: 0.8336 (mmm) REVERT: A 427 LEU cc_start: 0.9117 (tp) cc_final: 0.8766 (tt) REVERT: A 442 LYS cc_start: 0.9104 (mttp) cc_final: 0.8753 (mmtp) REVERT: A 633 TYR cc_start: 0.8547 (m-80) cc_final: 0.8133 (m-80) REVERT: A 639 ASP cc_start: 0.8088 (t0) cc_final: 0.7730 (t0) REVERT: A 643 GLU cc_start: 0.8483 (pm20) cc_final: 0.8047 (mp0) REVERT: A 650 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8217 (ptpt) REVERT: A 669 ASN cc_start: 0.9100 (t0) cc_final: 0.8875 (t0) REVERT: A 684 ASN cc_start: 0.9067 (t0) cc_final: 0.8334 (m-40) REVERT: A 709 PHE cc_start: 0.6847 (t80) cc_final: 0.6442 (t80) REVERT: B 2 GLU cc_start: 0.5420 (mp0) cc_final: 0.5216 (mp0) REVERT: B 80 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9075 (mmtm) REVERT: B 87 ILE cc_start: 0.9293 (pt) cc_final: 0.8762 (pt) REVERT: B 92 SER cc_start: 0.9329 (m) cc_final: 0.9044 (p) REVERT: B 112 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8181 (mp0) REVERT: B 133 ASP cc_start: 0.8145 (t70) cc_final: 0.7561 (m-30) REVERT: B 147 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8440 (tm-30) REVERT: B 151 ASP cc_start: 0.8266 (t0) cc_final: 0.7996 (t0) REVERT: B 155 GLU cc_start: 0.8564 (tt0) cc_final: 0.8336 (pt0) REVERT: B 174 GLU cc_start: 0.8757 (tt0) cc_final: 0.8325 (tm-30) REVERT: B 219 PHE cc_start: 0.8748 (t80) cc_final: 0.8484 (t80) REVERT: B 237 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8831 (mptt) REVERT: B 250 ILE cc_start: 0.8839 (mp) cc_final: 0.8612 (mp) REVERT: B 312 ASN cc_start: 0.9033 (m110) cc_final: 0.8228 (m-40) REVERT: B 320 TYR cc_start: 0.8137 (m-10) cc_final: 0.7656 (m-10) REVERT: B 336 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8521 (mttp) REVERT: B 408 MET cc_start: 0.8102 (ttm) cc_final: 0.7661 (ttp) REVERT: B 442 LEU cc_start: 0.8859 (tp) cc_final: 0.8219 (tp) REVERT: B 462 MET cc_start: 0.8288 (mtm) cc_final: 0.7882 (mtp) REVERT: B 528 MET cc_start: 0.8933 (mtt) cc_final: 0.8443 (mtt) REVERT: B 547 MET cc_start: 0.8651 (tpp) cc_final: 0.8192 (ttm) REVERT: B 574 MET cc_start: 0.8059 (mmm) cc_final: 0.7362 (tpp) REVERT: B 587 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7767 (mmtm) REVERT: B 629 ARG cc_start: 0.7953 (mpp-170) cc_final: 0.7308 (mtm180) REVERT: B 663 ARG cc_start: 0.6905 (tpp-160) cc_final: 0.5468 (tmt170) REVERT: B 681 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7208 (tt0) REVERT: B 736 TYR cc_start: 0.7336 (t80) cc_final: 0.6897 (t80) REVERT: C 51 MET cc_start: 0.8752 (tpp) cc_final: 0.8460 (tpp) REVERT: C 55 MET cc_start: 0.8555 (mmm) cc_final: 0.8209 (mmm) REVERT: C 85 LYS cc_start: 0.6357 (mmtm) cc_final: 0.5908 (mmmm) REVERT: C 103 THR cc_start: 0.9208 (p) cc_final: 0.8898 (t) REVERT: C 155 GLN cc_start: 0.8148 (tp40) cc_final: 0.7728 (mm-40) REVERT: C 160 LYS cc_start: 0.9139 (tttt) cc_final: 0.8910 (tttm) REVERT: C 232 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8177 (ttm110) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.1105 time to fit residues: 55.0358 Evaluate side-chains 292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105180 restraints weight = 28136.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108136 restraints weight = 16705.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110156 restraints weight = 11380.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111558 restraints weight = 8596.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112450 restraints weight = 7006.448| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12545 Z= 0.124 Angle : 0.649 9.350 16962 Z= 0.325 Chirality : 0.042 0.181 1855 Planarity : 0.004 0.054 2070 Dihedral : 11.186 73.518 1924 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1441 helix: 0.44 (0.20), residues: 664 sheet: -1.06 (0.53), residues: 98 loop : -2.28 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 723 TYR 0.023 0.002 TYR B 736 PHE 0.018 0.001 PHE B 108 TRP 0.027 0.002 TRP B 134 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00282 (12545) covalent geometry : angle 0.64927 (16962) hydrogen bonds : bond 0.04107 ( 531) hydrogen bonds : angle 4.45752 ( 1457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9127 (t80) cc_final: 0.8482 (t80) REVERT: A 235 ARG cc_start: 0.6854 (tpm170) cc_final: 0.6464 (mmm160) REVERT: A 297 MET cc_start: 0.7500 (mpp) cc_final: 0.5813 (mtm) REVERT: A 340 ASP cc_start: 0.8685 (t0) cc_final: 0.8453 (t70) REVERT: A 427 LEU cc_start: 0.9102 (tp) cc_final: 0.8853 (tt) REVERT: A 442 LYS cc_start: 0.9098 (mttp) cc_final: 0.8757 (mmtp) REVERT: A 453 GLU cc_start: 0.8131 (tp30) cc_final: 0.7906 (tp30) REVERT: A 633 TYR cc_start: 0.8464 (m-80) cc_final: 0.8223 (m-80) REVERT: A 643 GLU cc_start: 0.8397 (pm20) cc_final: 0.8133 (mp0) REVERT: A 650 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8284 (ptpt) REVERT: A 684 ASN cc_start: 0.9000 (t0) cc_final: 0.8204 (m-40) REVERT: A 709 PHE cc_start: 0.6957 (t80) cc_final: 0.6592 (t80) REVERT: B 78 LEU cc_start: 0.8882 (tp) cc_final: 0.8678 (tt) REVERT: B 80 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9080 (mmtm) REVERT: B 87 ILE cc_start: 0.9364 (pt) cc_final: 0.9123 (pt) REVERT: B 92 SER cc_start: 0.9399 (m) cc_final: 0.9107 (p) REVERT: B 112 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8169 (mp0) REVERT: B 133 ASP cc_start: 0.8207 (t70) cc_final: 0.7718 (m-30) REVERT: B 174 GLU cc_start: 0.8741 (tt0) cc_final: 0.8123 (tt0) REVERT: B 221 LYS cc_start: 0.8841 (tttt) cc_final: 0.8375 (tmtt) REVERT: B 237 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8849 (mptt) REVERT: B 250 ILE cc_start: 0.8847 (mp) cc_final: 0.8635 (mp) REVERT: B 320 TYR cc_start: 0.7847 (m-10) cc_final: 0.7561 (m-10) REVERT: B 336 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8513 (mttp) REVERT: B 408 MET cc_start: 0.8180 (ttm) cc_final: 0.7968 (ttp) REVERT: B 442 LEU cc_start: 0.8731 (tp) cc_final: 0.8177 (tp) REVERT: B 462 MET cc_start: 0.8136 (mtm) cc_final: 0.7885 (mtp) REVERT: B 547 MET cc_start: 0.8652 (tpp) cc_final: 0.8273 (ttm) REVERT: B 574 MET cc_start: 0.8105 (mmm) cc_final: 0.7420 (tpp) REVERT: B 587 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7941 (mmmt) REVERT: B 616 LEU cc_start: 0.8599 (mm) cc_final: 0.8367 (mp) REVERT: B 629 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7271 (mtm180) REVERT: B 663 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.5460 (tmt170) REVERT: B 681 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 10 GLU cc_start: 0.9192 (mp0) cc_final: 0.8642 (mp0) REVERT: C 51 MET cc_start: 0.8884 (tpp) cc_final: 0.8647 (tpp) REVERT: C 55 MET cc_start: 0.8605 (mmm) cc_final: 0.8277 (mmm) REVERT: C 85 LYS cc_start: 0.6375 (mmtm) cc_final: 0.5973 (mmmm) REVERT: C 155 GLN cc_start: 0.8176 (tp40) cc_final: 0.7763 (mm-40) REVERT: C 160 LYS cc_start: 0.9207 (tttt) cc_final: 0.8990 (tttm) REVERT: C 232 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8193 (ttm110) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1123 time to fit residues: 55.6189 Evaluate side-chains 288 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 141 optimal weight: 0.0370 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A 649 GLN B 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107420 restraints weight = 28247.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110512 restraints weight = 16756.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112618 restraints weight = 11388.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114035 restraints weight = 8573.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115096 restraints weight = 6966.330| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12545 Z= 0.116 Angle : 0.637 9.584 16962 Z= 0.318 Chirality : 0.042 0.157 1855 Planarity : 0.004 0.055 2070 Dihedral : 11.115 73.449 1924 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1441 helix: 0.56 (0.21), residues: 649 sheet: -1.08 (0.52), residues: 100 loop : -2.21 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 723 TYR 0.016 0.001 TYR B 736 PHE 0.019 0.001 PHE C 212 TRP 0.018 0.001 TRP B 134 HIS 0.004 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00255 (12545) covalent geometry : angle 0.63717 (16962) hydrogen bonds : bond 0.03889 ( 531) hydrogen bonds : angle 4.38308 ( 1457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.9111 (t80) cc_final: 0.8501 (t80) REVERT: A 297 MET cc_start: 0.7406 (mpp) cc_final: 0.5873 (mtm) REVERT: A 340 ASP cc_start: 0.8680 (t0) cc_final: 0.8477 (t70) REVERT: A 427 LEU cc_start: 0.8946 (tp) cc_final: 0.8677 (tt) REVERT: A 442 LYS cc_start: 0.9144 (mttp) cc_final: 0.8844 (mmtp) REVERT: A 453 GLU cc_start: 0.8071 (tp30) cc_final: 0.7823 (tp30) REVERT: A 457 PHE cc_start: 0.8773 (m-80) cc_final: 0.7829 (m-10) REVERT: A 549 TYR cc_start: 0.8083 (m-10) cc_final: 0.7845 (m-80) REVERT: A 643 GLU cc_start: 0.8302 (pm20) cc_final: 0.8028 (mp0) REVERT: A 650 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8454 (ptpt) REVERT: A 684 ASN cc_start: 0.8875 (t0) cc_final: 0.8181 (m-40) REVERT: A 709 PHE cc_start: 0.6847 (t80) cc_final: 0.6477 (t80) REVERT: B 41 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8946 (tm-30) REVERT: B 80 LYS cc_start: 0.9289 (mmmm) cc_final: 0.9069 (mmtm) REVERT: B 87 ILE cc_start: 0.9284 (pt) cc_final: 0.8851 (pt) REVERT: B 92 SER cc_start: 0.9448 (m) cc_final: 0.9175 (p) REVERT: B 120 MET cc_start: 0.6829 (ppp) cc_final: 0.6501 (ppp) REVERT: B 133 ASP cc_start: 0.7999 (t70) cc_final: 0.7638 (m-30) REVERT: B 147 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7971 (mt0) REVERT: B 172 ILE cc_start: 0.9604 (mm) cc_final: 0.9396 (mm) REVERT: B 174 GLU cc_start: 0.8698 (tt0) cc_final: 0.8292 (tt0) REVERT: B 320 TYR cc_start: 0.7818 (m-10) cc_final: 0.7532 (m-10) REVERT: B 336 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8563 (mttm) REVERT: B 402 CYS cc_start: 0.8165 (t) cc_final: 0.7784 (t) REVERT: B 403 PHE cc_start: 0.8863 (t80) cc_final: 0.8599 (t80) REVERT: B 423 MET cc_start: 0.9536 (mtp) cc_final: 0.9104 (mtp) REVERT: B 442 LEU cc_start: 0.8745 (tp) cc_final: 0.8217 (tp) REVERT: B 462 MET cc_start: 0.8293 (mtm) cc_final: 0.7990 (mtp) REVERT: B 547 MET cc_start: 0.8511 (tpp) cc_final: 0.8307 (ttm) REVERT: B 574 MET cc_start: 0.8081 (mmm) cc_final: 0.7431 (tpp) REVERT: B 587 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7918 (mmmt) REVERT: B 629 ARG cc_start: 0.7884 (mpp-170) cc_final: 0.7217 (mtm180) REVERT: B 663 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.6242 (tpp80) REVERT: B 681 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 7 LEU cc_start: 0.9197 (mt) cc_final: 0.8985 (mt) REVERT: C 10 GLU cc_start: 0.9208 (mp0) cc_final: 0.8593 (mp0) REVERT: C 32 TYR cc_start: 0.8120 (t80) cc_final: 0.7802 (t80) REVERT: C 55 MET cc_start: 0.8579 (mmm) cc_final: 0.8179 (mmm) REVERT: C 85 LYS cc_start: 0.6364 (mmtm) cc_final: 0.6089 (mmmm) REVERT: C 155 GLN cc_start: 0.8148 (tp40) cc_final: 0.7698 (mm-40) REVERT: C 232 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8213 (ttm110) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1117 time to fit residues: 57.2296 Evaluate side-chains 294 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN A 640 ASN B 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103731 restraints weight = 28241.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106682 restraints weight = 16876.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108702 restraints weight = 11537.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109988 restraints weight = 8724.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111041 restraints weight = 7162.298| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12545 Z= 0.148 Angle : 0.666 10.286 16962 Z= 0.337 Chirality : 0.043 0.162 1855 Planarity : 0.005 0.060 2070 Dihedral : 11.137 73.573 1924 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 0.08 % Allowed : 0.54 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.22), residues: 1441 helix: 0.55 (0.21), residues: 648 sheet: -1.41 (0.47), residues: 113 loop : -2.15 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 235 TYR 0.022 0.002 TYR A 208 PHE 0.015 0.001 PHE A 709 TRP 0.039 0.002 TRP C 53 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00338 (12545) covalent geometry : angle 0.66624 (16962) hydrogen bonds : bond 0.04219 ( 531) hydrogen bonds : angle 4.51137 ( 1457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.48 seconds wall clock time: 37 minutes 4.64 seconds (2224.64 seconds total)