Starting phenix.real_space_refine on Wed Jul 30 15:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_9579_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_9579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_9579.map" model { file = "/net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_9579_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kup_9579/07_2025/6kup_9579_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 7.07, per 1000 atoms: 0.58 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.56 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: 3.81 Time building geometry restraints manager: 3.20 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: 0.350 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP A 386 HIS 0.007 0.002 HIS B 606 PHE 0.026 0.002 PHE B 726 TYR 0.018 0.002 TYR A 549 ARG 0.007 0.001 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.14526 ( 531) hydrogen bonds : angle 9.05112 ( 1457) covalent geometry : bond 0.00409 (12545) covalent geometry : angle 0.80867 (16962) *********************** 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 : 1.270 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: 0.7100 (t-100) REVERT: A 278 ASP cc_start: 0.8685 (t0) cc_final: 0.8421 (t0) REVERT: A 288 LEU cc_start: 0.9683 (tp) cc_final: 0.9456 (tt) REVERT: A 364 GLU cc_start: 0.8341 (mp0) cc_final: 0.8054 (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: 0.8254 (t-100) REVERT: A 453 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7672 (tp30) REVERT: A 495 ASP cc_start: 0.8666 (m-30) cc_final: 0.8175 (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: 0.7758 (mmm) REVERT: A 562 TRP cc_start: 0.7924 (m100) cc_final: 0.7213 (m100) REVERT: A 578 GLU cc_start: 0.8803 (tt0) cc_final: 0.8427 (tt0) REVERT: A 600 LYS cc_start: 0.9278 (tppt) cc_final: 0.8777 (tptp) REVERT: A 601 ARG cc_start: 0.8753 (mmt180) cc_final: 0.8531 (mmm160) REVERT: A 639 ASP cc_start: 0.7436 (m-30) cc_final: 0.6536 (m-30) REVERT: A 650 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8328 (mtmt) REVERT: A 661 ASP cc_start: 0.7648 (t0) cc_final: 0.7441 (t0) REVERT: A 684 ASN cc_start: 0.9318 (t0) cc_final: 0.9100 (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: 0.8005 (ttp-170) REVERT: B 52 THR cc_start: 0.8465 (t) cc_final: 0.8185 (t) REVERT: B 85 VAL cc_start: 0.9349 (t) cc_final: 0.8883 (t) REVERT: B 147 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8248 (mm-40) REVERT: B 151 ASP cc_start: 0.8473 (t0) cc_final: 0.7640 (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: 0.7682 (mtmm) REVERT: B 234 GLU cc_start: 0.7109 (tt0) cc_final: 0.6434 (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: 0.8184 (tptt) REVERT: B 311 TRP cc_start: 0.9365 (t-100) cc_final: 0.9082 (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: 0.9164 (tp) REVERT: B 410 MET cc_start: 0.5922 (mtp) cc_final: 0.5690 (mtt) REVERT: B 541 SER cc_start: 0.8831 (p) cc_final: 0.8033 (p) REVERT: B 576 ILE cc_start: 0.9376 (mt) cc_final: 0.8946 (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: 0.7889 (pm20) REVERT: B 612 LEU cc_start: 0.8521 (tp) cc_final: 0.7929 (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: 0.8253 (m) REVERT: B 736 TYR cc_start: 0.8102 (t80) cc_final: 0.6475 (t80) REVERT: C 55 MET cc_start: 0.8368 (mmm) cc_final: 0.8087 (mmm) REVERT: C 85 LYS cc_start: 0.5817 (mmtm) cc_final: 0.4829 (ptpt) REVERT: C 96 LEU cc_start: 0.8227 (mt) cc_final: 0.7921 (mt) REVERT: C 102 ILE cc_start: 0.8970 (mt) cc_final: 0.8578 (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: 0.6825 (m-80) REVERT: C 247 TRP cc_start: 0.8394 (p-90) cc_final: 0.7657 (p90) outliers start: 2 outliers final: 0 residues processed: 566 average time/residue: 0.2851 time to fit residues: 217.5168 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 : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.0060 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 640 ASN B 70 ASN B 147 GLN B 477 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112340 restraints weight = 27196.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115714 restraints weight = 15555.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117976 restraints weight = 10363.432| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12545 Z= 0.128 Angle : 0.626 13.023 16962 Z= 0.321 Chirality : 0.041 0.163 1855 Planarity : 0.005 0.057 2070 Dihedral : 11.525 74.237 1924 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.19), residues: 1441 helix: -1.12 (0.18), residues: 660 sheet: -1.61 (0.54), residues: 96 loop : -2.92 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 386 HIS 0.005 0.001 HIS C 216 PHE 0.026 0.001 PHE B 108 TYR 0.035 0.002 TYR B 736 ARG 0.009 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 531) hydrogen bonds : angle 5.19194 ( 1457) covalent geometry : bond 0.00267 (12545) covalent geometry : angle 0.62587 (16962) *********************** 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 445 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.269 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 271 TRP cc_start: 0.7336 (t-100) cc_final: 0.6936 (t-100) REVERT: A 315 TYR cc_start: 0.8155 (m-80) cc_final: 0.7821 (m-80) REVERT: A 386 TRP cc_start: 0.8846 (t-100) cc_final: 0.7970 (t-100) REVERT: A 390 MET cc_start: 0.8550 (ptm) cc_final: 0.7553 (ttm) REVERT: A 402 ASP cc_start: 0.7031 (m-30) cc_final: 0.6703 (m-30) REVERT: A 440 MET cc_start: 0.8720 (mtm) cc_final: 0.8508 (mtm) REVERT: A 453 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7573 (tp30) REVERT: A 547 PHE cc_start: 0.8858 (m-80) cc_final: 0.8269 (m-10) REVERT: A 558 LEU cc_start: 0.8799 (tt) cc_final: 0.8570 (tt) REVERT: A 591 ASN cc_start: 0.8411 (t0) cc_final: 0.8210 (t0) REVERT: A 643 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7423 (mm-30) REVERT: A 654 MET cc_start: 0.8648 (tpp) cc_final: 0.8188 (tpp) REVERT: A 684 ASN cc_start: 0.9195 (t0) cc_final: 0.8598 (m-40) REVERT: A 692 ASP cc_start: 0.8258 (t0) cc_final: 0.7989 (t0) REVERT: B 2 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6968 (mt-10) REVERT: B 41 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 45 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7864 (mtp180) REVERT: B 52 THR cc_start: 0.8464 (t) cc_final: 0.8169 (t) REVERT: B 85 VAL cc_start: 0.9146 (t) cc_final: 0.8852 (t) REVERT: B 90 MET cc_start: 0.9124 (ptm) cc_final: 0.8573 (ptm) REVERT: B 92 SER cc_start: 0.9236 (m) cc_final: 0.8992 (p) REVERT: B 119 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7068 (tptt) REVERT: B 133 ASP cc_start: 0.8146 (t70) cc_final: 0.7686 (m-30) REVERT: B 151 ASP cc_start: 0.8551 (t0) cc_final: 0.7863 (t70) REVERT: B 174 GLU cc_start: 0.8636 (tt0) cc_final: 0.8269 (tt0) REVERT: B 234 GLU cc_start: 0.6967 (tt0) cc_final: 0.6374 (pm20) REVERT: B 237 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8358 (mptt) REVERT: B 255 LYS cc_start: 0.8756 (tptt) cc_final: 0.8387 (tptt) REVERT: B 270 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7075 (mp0) REVERT: B 312 ASN cc_start: 0.8965 (m-40) cc_final: 0.8306 (m-40) REVERT: B 324 LEU cc_start: 0.9452 (mp) cc_final: 0.9241 (mp) REVERT: B 408 MET cc_start: 0.6662 (ttm) cc_final: 0.6195 (ttp) REVERT: B 453 ILE cc_start: 0.9100 (pt) cc_final: 0.8833 (tp) REVERT: B 460 MET cc_start: 0.8485 (tpp) cc_final: 0.8276 (tpp) REVERT: B 528 MET cc_start: 0.8833 (mtm) cc_final: 0.8433 (mtp) REVERT: B 560 TYR cc_start: 0.8495 (m-10) cc_final: 0.8163 (m-10) REVERT: B 578 ARG cc_start: 0.7849 (tpp80) cc_final: 0.6933 (ptm-80) REVERT: B 587 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7943 (mmmt) REVERT: B 591 LEU cc_start: 0.9168 (tp) cc_final: 0.8844 (tp) REVERT: B 661 SER cc_start: 0.9089 (m) cc_final: 0.8636 (t) REVERT: B 681 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 51 MET cc_start: 0.8969 (tpp) cc_final: 0.8639 (tpp) REVERT: C 55 MET cc_start: 0.8357 (mmm) cc_final: 0.7952 (mmm) REVERT: C 85 LYS cc_start: 0.5533 (mmtm) cc_final: 0.4228 (ptpt) REVERT: C 213 MET cc_start: 0.9201 (ptm) cc_final: 0.8765 (ppp) REVERT: C 214 ILE cc_start: 0.9314 (mt) cc_final: 0.8977 (mt) REVERT: C 232 ARG cc_start: 0.8537 (ttm110) cc_final: 0.8202 (ttp-110) REVERT: C 242 LEU cc_start: 0.8697 (tt) cc_final: 0.8492 (tt) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2681 time to fit residues: 163.4721 Evaluate side-chains 331 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 61 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 649 GLN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107294 restraints weight = 28039.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110539 restraints weight = 16236.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112809 restraints weight = 10885.481| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12545 Z= 0.137 Angle : 0.598 10.617 16962 Z= 0.308 Chirality : 0.041 0.155 1855 Planarity : 0.004 0.045 2070 Dihedral : 11.393 74.130 1924 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 0.23 % Allowed : 2.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1441 helix: -0.08 (0.20), residues: 662 sheet: -1.38 (0.52), residues: 100 loop : -2.70 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 562 HIS 0.007 0.001 HIS C 216 PHE 0.013 0.001 PHE A 481 TYR 0.012 0.001 TYR A 205 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 531) hydrogen bonds : angle 4.66567 ( 1457) covalent geometry : bond 0.00305 (12545) covalent geometry : angle 0.59776 (16962) *********************** 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 386 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 1.331 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 235 ARG cc_start: 0.7053 (tpm170) cc_final: 0.6589 (tpm170) REVERT: A 271 TRP cc_start: 0.7356 (t-100) cc_final: 0.6947 (t-100) REVERT: A 315 TYR cc_start: 0.8172 (m-80) cc_final: 0.7933 (m-80) REVERT: A 340 ASP cc_start: 0.8622 (t0) cc_final: 0.8297 (t70) REVERT: A 364 GLU cc_start: 0.8199 (mp0) cc_final: 0.7817 (mp0) REVERT: A 406 MET cc_start: 0.7771 (tpp) cc_final: 0.6900 (mtt) REVERT: A 417 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 428 GLU cc_start: 0.7598 (tp30) cc_final: 0.7093 (tp30) REVERT: A 453 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7515 (tp30) REVERT: A 547 PHE cc_start: 0.8774 (m-80) cc_final: 0.8254 (m-80) REVERT: A 557 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8446 (ttmt) REVERT: A 643 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7499 (mm-30) REVERT: A 649 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: A 650 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8381 (ptpt) REVERT: A 653 LEU cc_start: 0.9108 (mp) cc_final: 0.8864 (mp) REVERT: A 654 MET cc_start: 0.8456 (tpp) cc_final: 0.8221 (tpp) REVERT: A 684 ASN cc_start: 0.9194 (t0) cc_final: 0.8904 (t0) REVERT: A 708 TYR cc_start: 0.8672 (m-80) cc_final: 0.8311 (m-80) REVERT: B 10 LEU cc_start: 0.9377 (tt) cc_final: 0.9165 (mm) REVERT: B 22 TYR cc_start: 0.9049 (m-80) cc_final: 0.8722 (m-10) REVERT: B 52 THR cc_start: 0.8412 (t) cc_final: 0.8182 (t) REVERT: B 78 LEU cc_start: 0.8801 (tp) cc_final: 0.8292 (tp) REVERT: B 80 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9115 (mmtm) REVERT: B 87 ILE cc_start: 0.9312 (pt) cc_final: 0.9099 (pt) REVERT: B 90 MET cc_start: 0.9059 (ptm) cc_final: 0.8819 (ptm) REVERT: B 92 SER cc_start: 0.9334 (m) cc_final: 0.9058 (p) REVERT: B 133 ASP cc_start: 0.8247 (t70) cc_final: 0.7857 (m-30) REVERT: B 174 GLU cc_start: 0.8740 (tt0) cc_final: 0.8503 (tt0) REVERT: B 183 PHE cc_start: 0.8612 (p90) cc_final: 0.8036 (p90) REVERT: B 184 LYS cc_start: 0.9006 (ptmt) cc_final: 0.8779 (ptpp) REVERT: B 221 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9127 (mtmt) REVERT: B 234 GLU cc_start: 0.7011 (tt0) cc_final: 0.6723 (pm20) REVERT: B 237 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8520 (mptt) REVERT: B 250 ILE cc_start: 0.8613 (mp) cc_final: 0.8411 (mp) REVERT: B 255 LYS cc_start: 0.8695 (tptt) cc_final: 0.8389 (tptt) REVERT: B 312 ASN cc_start: 0.8863 (m-40) cc_final: 0.8178 (m-40) REVERT: B 320 TYR cc_start: 0.8347 (m-10) cc_final: 0.8085 (m-10) REVERT: B 335 MET cc_start: 0.7773 (mmm) cc_final: 0.7512 (mmm) REVERT: B 339 CYS cc_start: 0.8453 (m) cc_final: 0.8073 (m) REVERT: B 375 MET cc_start: 0.8828 (mtp) cc_final: 0.8538 (mtp) REVERT: B 389 LEU cc_start: 0.9151 (tp) cc_final: 0.8909 (tt) REVERT: B 408 MET cc_start: 0.6699 (ttm) cc_final: 0.6256 (ttp) REVERT: B 453 ILE cc_start: 0.8932 (pt) cc_final: 0.8674 (tp) REVERT: B 460 MET cc_start: 0.8688 (tpp) cc_final: 0.8443 (tpp) REVERT: B 461 GLU cc_start: 0.8019 (pt0) cc_final: 0.7485 (pt0) REVERT: B 496 MET cc_start: 0.8572 (mtp) cc_final: 0.8218 (mtp) REVERT: B 520 GLU cc_start: 0.8386 (mp0) cc_final: 0.7620 (mp0) REVERT: B 528 MET cc_start: 0.9157 (mtm) cc_final: 0.8951 (mtp) REVERT: B 578 ARG cc_start: 0.7795 (tpp80) cc_final: 0.6903 (ptm-80) REVERT: B 663 ARG cc_start: 0.6427 (tpp-160) cc_final: 0.6184 (tpp-160) REVERT: B 681 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 749 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6850 (tm-30) REVERT: C 32 TYR cc_start: 0.8078 (t80) cc_final: 0.7596 (t80) REVERT: C 55 MET cc_start: 0.8659 (mmm) cc_final: 0.8194 (mmm) REVERT: C 81 ASP cc_start: 0.7677 (t0) cc_final: 0.7285 (t0) REVERT: C 85 LYS cc_start: 0.5631 (mmtm) cc_final: 0.4451 (ptpt) REVERT: C 102 ILE cc_start: 0.9032 (mt) cc_final: 0.8787 (mp) REVERT: C 103 THR cc_start: 0.9246 (p) cc_final: 0.8881 (t) REVERT: C 213 MET cc_start: 0.9189 (ptm) cc_final: 0.8687 (ppp) REVERT: C 218 PHE cc_start: 0.8326 (m-10) cc_final: 0.7075 (m-80) outliers start: 3 outliers final: 0 residues processed: 383 average time/residue: 0.3300 time to fit residues: 179.5564 Evaluate side-chains 309 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 308 ASN B 312 ASN B 383 ASN C 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104282 restraints weight = 27703.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107345 restraints weight = 16340.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109426 restraints weight = 11164.546| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12545 Z= 0.168 Angle : 0.620 10.864 16962 Z= 0.320 Chirality : 0.042 0.163 1855 Planarity : 0.004 0.061 2070 Dihedral : 11.374 74.094 1924 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.15 % Favored : 92.78 % Rotamer: Outliers : 0.08 % Allowed : 2.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.21), residues: 1441 helix: 0.26 (0.20), residues: 669 sheet: -1.47 (0.53), residues: 100 loop : -2.66 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 38 HIS 0.006 0.001 HIS C 216 PHE 0.024 0.002 PHE B 108 TYR 0.017 0.002 TYR B 6 ARG 0.009 0.001 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 531) hydrogen bonds : angle 4.59901 ( 1457) covalent geometry : bond 0.00373 (12545) covalent geometry : angle 0.62035 (16962) *********************** 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 359 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 3.721 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 193 PHE cc_start: 0.9101 (t80) cc_final: 0.8762 (t80) REVERT: A 332 GLU cc_start: 0.7522 (pt0) cc_final: 0.6949 (pm20) REVERT: A 340 ASP cc_start: 0.8751 (t0) cc_final: 0.8478 (t70) REVERT: A 364 GLU cc_start: 0.8338 (mp0) cc_final: 0.8061 (mp0) REVERT: A 417 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8348 (mt-10) REVERT: A 557 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8460 (ttmt) REVERT: A 643 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8256 (mp0) REVERT: A 656 LEU cc_start: 0.9468 (tt) cc_final: 0.9168 (tp) REVERT: A 708 TYR cc_start: 0.8633 (m-80) cc_final: 0.8339 (m-80) REVERT: B 4 ASN cc_start: 0.9249 (t0) cc_final: 0.8788 (t0) REVERT: B 10 LEU cc_start: 0.9388 (tt) cc_final: 0.9177 (mm) REVERT: B 52 THR cc_start: 0.8654 (t) cc_final: 0.8416 (t) REVERT: B 65 ARG cc_start: 0.7595 (ttm170) cc_final: 0.6835 (ttm-80) REVERT: B 78 LEU cc_start: 0.8755 (tp) cc_final: 0.8228 (tp) REVERT: B 80 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9081 (mmtm) REVERT: B 90 MET cc_start: 0.9133 (ptm) cc_final: 0.8925 (ptm) REVERT: B 92 SER cc_start: 0.9337 (m) cc_final: 0.9048 (p) REVERT: B 112 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8355 (mp0) REVERT: B 133 ASP cc_start: 0.8438 (t70) cc_final: 0.8130 (m-30) REVERT: B 174 GLU cc_start: 0.8847 (tt0) cc_final: 0.8602 (tt0) REVERT: B 184 LYS cc_start: 0.8835 (ptmt) cc_final: 0.8627 (ptpp) REVERT: B 237 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8567 (mptt) REVERT: B 250 ILE cc_start: 0.8781 (mp) cc_final: 0.8530 (mp) REVERT: B 312 ASN cc_start: 0.8924 (m110) cc_final: 0.8342 (m-40) REVERT: B 320 TYR cc_start: 0.8394 (m-10) cc_final: 0.8043 (m-10) REVERT: B 328 THR cc_start: 0.8597 (p) cc_final: 0.8361 (m) REVERT: B 349 LYS cc_start: 0.9184 (pttm) cc_final: 0.8949 (ptpp) REVERT: B 370 ILE cc_start: 0.9047 (mm) cc_final: 0.8523 (tp) REVERT: B 375 MET cc_start: 0.8839 (mtp) cc_final: 0.8499 (mtp) REVERT: B 383 ASN cc_start: 0.8437 (m-40) cc_final: 0.8168 (m110) REVERT: B 408 MET cc_start: 0.7411 (ttm) cc_final: 0.7135 (ttm) REVERT: B 442 LEU cc_start: 0.8810 (tp) cc_final: 0.8157 (tp) REVERT: B 462 MET cc_start: 0.8412 (mtm) cc_final: 0.8046 (mtp) REVERT: B 496 MET cc_start: 0.8738 (mtp) cc_final: 0.8372 (mtt) REVERT: B 520 GLU cc_start: 0.8399 (mp0) cc_final: 0.7555 (mp0) REVERT: B 547 MET cc_start: 0.9117 (tpp) cc_final: 0.8654 (ttm) REVERT: B 587 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8011 (mmmt) REVERT: B 599 MET cc_start: 0.8657 (tpp) cc_final: 0.8106 (tpt) REVERT: B 611 ILE cc_start: 0.8421 (mt) cc_final: 0.8145 (mt) REVERT: B 681 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7597 (mm-30) REVERT: C 32 TYR cc_start: 0.8161 (t80) cc_final: 0.7725 (t80) REVERT: C 55 MET cc_start: 0.8700 (mmm) cc_final: 0.8359 (mmm) REVERT: C 85 LYS cc_start: 0.5935 (mmtm) cc_final: 0.4696 (ptpt) REVERT: C 102 ILE cc_start: 0.9143 (mt) cc_final: 0.8899 (mp) REVERT: C 103 THR cc_start: 0.9225 (p) cc_final: 0.8847 (t) REVERT: C 118 ILE cc_start: 0.8766 (mt) cc_final: 0.8519 (mt) REVERT: C 155 GLN cc_start: 0.8556 (tp40) cc_final: 0.8203 (tp40) REVERT: C 213 MET cc_start: 0.9200 (ptm) cc_final: 0.8797 (ppp) REVERT: C 218 PHE cc_start: 0.8459 (m-10) cc_final: 0.7276 (m-80) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.3366 time to fit residues: 171.2645 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 : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 HIS A 649 GLN B 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105643 restraints weight = 27796.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108704 restraints weight = 16635.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110797 restraints weight = 11431.954| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5320 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= 0.133 Angle : 0.594 9.860 16962 Z= 0.305 Chirality : 0.041 0.149 1855 Planarity : 0.004 0.061 2070 Dihedral : 11.275 73.815 1924 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1441 helix: 0.52 (0.21), residues: 663 sheet: -1.33 (0.53), residues: 105 loop : -2.44 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 38 HIS 0.005 0.001 HIS C 216 PHE 0.021 0.001 PHE B 108 TYR 0.015 0.001 TYR B 736 ARG 0.007 0.001 ARG C 133 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 531) hydrogen bonds : angle 4.53221 ( 1457) covalent geometry : bond 0.00302 (12545) covalent geometry : angle 0.59357 (16962) *********************** 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 356 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 3.170 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 193 PHE cc_start: 0.9074 (t80) cc_final: 0.8746 (t80) REVERT: A 275 LYS cc_start: 0.8975 (pttp) cc_final: 0.8268 (pptt) REVERT: A 332 GLU cc_start: 0.7308 (pt0) cc_final: 0.6963 (pm20) REVERT: A 340 ASP cc_start: 0.8744 (t0) cc_final: 0.8441 (t70) REVERT: A 409 MET cc_start: 0.8644 (mmm) cc_final: 0.8371 (mmm) REVERT: A 453 GLU cc_start: 0.8187 (tp30) cc_final: 0.7931 (tp30) REVERT: A 526 VAL cc_start: 0.9115 (t) cc_final: 0.8908 (t) REVERT: A 684 ASN cc_start: 0.9221 (t0) cc_final: 0.8612 (m110) REVERT: A 708 TYR cc_start: 0.8631 (m-80) cc_final: 0.8381 (m-80) REVERT: B 1 MET cc_start: 0.7788 (tmm) cc_final: 0.7548 (tmm) REVERT: B 4 ASN cc_start: 0.9190 (t0) cc_final: 0.8813 (t0) REVERT: B 10 LEU cc_start: 0.9418 (tt) cc_final: 0.9100 (mm) REVERT: B 52 THR cc_start: 0.8597 (t) cc_final: 0.8338 (t) REVERT: B 78 LEU cc_start: 0.8746 (tp) cc_final: 0.8500 (tp) REVERT: B 80 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9120 (mmtm) REVERT: B 90 MET cc_start: 0.9128 (ptm) cc_final: 0.8842 (ptm) REVERT: B 112 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8332 (mp0) REVERT: B 133 ASP cc_start: 0.8400 (t70) cc_final: 0.8068 (m-30) REVERT: B 147 GLN cc_start: 0.8563 (tp40) cc_final: 0.8343 (tm-30) REVERT: B 237 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8570 (mptt) REVERT: B 250 ILE cc_start: 0.8800 (mp) cc_final: 0.8596 (mp) REVERT: B 312 ASN cc_start: 0.9004 (m110) cc_final: 0.8330 (m-40) REVERT: B 320 TYR cc_start: 0.8337 (m-10) cc_final: 0.7932 (m-10) REVERT: B 336 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8747 (ptmt) REVERT: B 370 ILE cc_start: 0.9045 (mm) cc_final: 0.8545 (tp) REVERT: B 375 MET cc_start: 0.8736 (mtp) cc_final: 0.8458 (mtp) REVERT: B 402 CYS cc_start: 0.8315 (t) cc_final: 0.8059 (t) REVERT: B 408 MET cc_start: 0.7679 (ttm) cc_final: 0.7158 (ttp) REVERT: B 462 MET cc_start: 0.8177 (mtm) cc_final: 0.7839 (mtp) REVERT: B 496 MET cc_start: 0.8755 (mtp) cc_final: 0.8486 (mtt) REVERT: B 520 GLU cc_start: 0.8437 (mp0) cc_final: 0.7616 (mp0) REVERT: B 587 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8082 (mmmt) REVERT: B 611 ILE cc_start: 0.8506 (mt) cc_final: 0.8225 (mt) REVERT: B 681 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 55 MET cc_start: 0.8621 (mmm) cc_final: 0.8232 (mmm) REVERT: C 75 GLU cc_start: 0.7520 (pp20) cc_final: 0.6929 (pm20) REVERT: C 85 LYS cc_start: 0.6127 (mmtm) cc_final: 0.5768 (mmmm) REVERT: C 102 ILE cc_start: 0.9154 (mt) cc_final: 0.8911 (mp) REVERT: C 103 THR cc_start: 0.9223 (p) cc_final: 0.8823 (t) REVERT: C 155 GLN cc_start: 0.8476 (tp40) cc_final: 0.8150 (tp40) REVERT: C 213 MET cc_start: 0.9062 (ptm) cc_final: 0.8700 (ppp) REVERT: C 218 PHE cc_start: 0.8420 (m-10) cc_final: 0.7350 (m-80) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.3798 time to fit residues: 196.6013 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 : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 66 optimal weight: 0.6980 chunk 136 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 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 = 0.3769 r_free = 0.3769 target = 0.130227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107123 restraints weight = 28282.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110261 restraints weight = 16695.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112433 restraints weight = 11312.705| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12545 Z= 0.111 Angle : 0.581 10.083 16962 Z= 0.296 Chirality : 0.040 0.156 1855 Planarity : 0.004 0.059 2070 Dihedral : 11.197 73.625 1924 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1441 helix: 0.69 (0.21), residues: 654 sheet: -1.37 (0.58), residues: 90 loop : -2.31 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 83 HIS 0.005 0.001 HIS C 216 PHE 0.018 0.001 PHE B 108 TYR 0.020 0.001 TYR B 6 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 531) hydrogen bonds : angle 4.32212 ( 1457) covalent geometry : bond 0.00247 (12545) covalent geometry : angle 0.58111 (16962) *********************** 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 364 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.459 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 188 TYR cc_start: 0.8985 (t80) cc_final: 0.8759 (t80) REVERT: A 193 PHE cc_start: 0.8982 (t80) cc_final: 0.8563 (t80) REVERT: A 340 ASP cc_start: 0.8715 (t0) cc_final: 0.8425 (t70) REVERT: A 633 TYR cc_start: 0.8578 (m-80) cc_final: 0.8300 (m-80) REVERT: A 639 ASP cc_start: 0.7787 (t70) cc_final: 0.7447 (t70) REVERT: A 650 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8253 (ptpt) REVERT: A 656 LEU cc_start: 0.9414 (tt) cc_final: 0.9211 (tp) REVERT: A 684 ASN cc_start: 0.9168 (t0) cc_final: 0.8482 (m-40) REVERT: A 708 TYR cc_start: 0.8590 (m-80) cc_final: 0.8304 (m-80) REVERT: B 1 MET cc_start: 0.7727 (tmm) cc_final: 0.7512 (tmm) REVERT: B 10 LEU cc_start: 0.9393 (tt) cc_final: 0.9074 (mm) REVERT: B 52 THR cc_start: 0.8517 (t) cc_final: 0.8272 (t) REVERT: B 80 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9102 (mmtm) REVERT: B 85 VAL cc_start: 0.9143 (t) cc_final: 0.8934 (t) REVERT: B 87 ILE cc_start: 0.9280 (pt) cc_final: 0.8748 (pt) REVERT: B 133 ASP cc_start: 0.8382 (t70) cc_final: 0.7979 (m-30) REVERT: B 155 GLU cc_start: 0.7903 (pp20) cc_final: 0.7633 (pp20) REVERT: B 172 ILE cc_start: 0.9657 (mm) cc_final: 0.9412 (mm) REVERT: B 174 GLU cc_start: 0.8539 (tt0) cc_final: 0.7672 (tm-30) REVERT: B 178 TRP cc_start: 0.7663 (m-10) cc_final: 0.6786 (m-10) REVERT: B 219 PHE cc_start: 0.8930 (t80) cc_final: 0.8559 (t80) REVERT: B 237 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8785 (mptt) REVERT: B 250 ILE cc_start: 0.8800 (mp) cc_final: 0.8524 (mp) REVERT: B 312 ASN cc_start: 0.8986 (m110) cc_final: 0.8203 (m-40) REVERT: B 320 TYR cc_start: 0.8208 (m-10) cc_final: 0.7851 (m-10) REVERT: B 336 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8293 (mttp) REVERT: B 370 ILE cc_start: 0.9023 (mm) cc_final: 0.8529 (tp) REVERT: B 375 MET cc_start: 0.8786 (mtp) cc_final: 0.8544 (mtp) REVERT: B 383 ASN cc_start: 0.8570 (m-40) cc_final: 0.8346 (m110) REVERT: B 408 MET cc_start: 0.7550 (ttm) cc_final: 0.7024 (ttp) REVERT: B 442 LEU cc_start: 0.8818 (tp) cc_final: 0.8139 (tp) REVERT: B 462 MET cc_start: 0.8235 (mtm) cc_final: 0.7781 (mtp) REVERT: B 496 MET cc_start: 0.8732 (mtp) cc_final: 0.8454 (mtt) REVERT: B 520 GLU cc_start: 0.8326 (mp0) cc_final: 0.7567 (mp0) REVERT: B 547 MET cc_start: 0.8899 (tpp) cc_final: 0.8557 (ttm) REVERT: B 587 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7934 (mmmt) REVERT: B 611 ILE cc_start: 0.8399 (mt) cc_final: 0.8193 (mt) REVERT: B 629 ARG cc_start: 0.7915 (mpp-170) cc_final: 0.7183 (mtm180) REVERT: B 663 ARG cc_start: 0.6633 (tpp-160) cc_final: 0.5408 (tmt170) REVERT: B 681 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7408 (mm-30) REVERT: C 55 MET cc_start: 0.8524 (mmm) cc_final: 0.8244 (mmm) REVERT: C 85 LYS cc_start: 0.6134 (mmtm) cc_final: 0.5725 (mmmm) REVERT: C 102 ILE cc_start: 0.9122 (mt) cc_final: 0.8896 (mp) REVERT: C 103 THR cc_start: 0.9260 (p) cc_final: 0.8805 (t) REVERT: C 155 GLN cc_start: 0.8348 (tp40) cc_final: 0.8019 (tp40) REVERT: C 166 ILE cc_start: 0.9193 (tp) cc_final: 0.8948 (tp) REVERT: C 213 MET cc_start: 0.9079 (ptm) cc_final: 0.8756 (ppp) REVERT: C 218 PHE cc_start: 0.8362 (m-10) cc_final: 0.7254 (m-80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2595 time to fit residues: 133.3273 Evaluate side-chains 306 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107238 restraints weight = 27710.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110413 restraints weight = 16310.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112719 restraints weight = 11088.246| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12545 Z= 0.119 Angle : 0.601 8.203 16962 Z= 0.305 Chirality : 0.041 0.153 1855 Planarity : 0.004 0.058 2070 Dihedral : 11.164 73.600 1924 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1441 helix: 0.66 (0.21), residues: 658 sheet: -1.26 (0.51), residues: 106 loop : -2.28 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 83 HIS 0.005 0.001 HIS B 121 PHE 0.020 0.001 PHE B 108 TYR 0.013 0.001 TYR A 261 ARG 0.006 0.001 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 531) hydrogen bonds : angle 4.34039 ( 1457) covalent geometry : bond 0.00268 (12545) covalent geometry : angle 0.60117 (16962) *********************** 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 355 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.407 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 188 TYR cc_start: 0.9013 (t80) cc_final: 0.8658 (t80) REVERT: A 193 PHE cc_start: 0.9092 (t80) cc_final: 0.8655 (t80) REVERT: A 278 ASP cc_start: 0.8592 (t0) cc_final: 0.8263 (t0) REVERT: A 332 GLU cc_start: 0.7147 (pt0) cc_final: 0.6866 (pm20) REVERT: A 340 ASP cc_start: 0.8731 (t0) cc_final: 0.8439 (t70) REVERT: A 453 GLU cc_start: 0.8070 (tp30) cc_final: 0.7844 (tp30) REVERT: A 495 ASP cc_start: 0.8344 (m-30) cc_final: 0.7938 (m-30) REVERT: A 517 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8136 (tppt) REVERT: A 633 TYR cc_start: 0.8597 (m-80) cc_final: 0.8343 (m-80) REVERT: A 649 GLN cc_start: 0.8770 (tt0) cc_final: 0.8107 (tm-30) REVERT: A 650 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8269 (ptpt) REVERT: A 684 ASN cc_start: 0.9222 (t0) cc_final: 0.8497 (m110) REVERT: A 692 ASP cc_start: 0.8719 (t0) cc_final: 0.8413 (t0) REVERT: B 4 ASN cc_start: 0.9231 (t0) cc_final: 0.9019 (t0) REVERT: B 10 LEU cc_start: 0.9366 (tt) cc_final: 0.9131 (mm) REVERT: B 78 LEU cc_start: 0.8767 (tp) cc_final: 0.8531 (tt) REVERT: B 80 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9117 (mmtm) REVERT: B 87 ILE cc_start: 0.9360 (pt) cc_final: 0.9129 (pt) REVERT: B 90 MET cc_start: 0.8941 (ptm) cc_final: 0.8719 (ptm) REVERT: B 112 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8294 (mp0) REVERT: B 120 MET cc_start: 0.5304 (ppp) cc_final: 0.4697 (ppp) REVERT: B 133 ASP cc_start: 0.8281 (t70) cc_final: 0.7940 (m-30) REVERT: B 155 GLU cc_start: 0.7786 (pp20) cc_final: 0.7535 (pp20) REVERT: B 174 GLU cc_start: 0.8765 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 178 TRP cc_start: 0.7737 (m-10) cc_final: 0.6761 (m-10) REVERT: B 237 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8806 (mptt) REVERT: B 312 ASN cc_start: 0.8940 (m110) cc_final: 0.8121 (m-40) REVERT: B 320 TYR cc_start: 0.8209 (m-10) cc_final: 0.7621 (m-10) REVERT: B 336 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8401 (mttp) REVERT: B 370 ILE cc_start: 0.9019 (mm) cc_final: 0.8557 (tp) REVERT: B 408 MET cc_start: 0.7985 (ttm) cc_final: 0.7439 (ttp) REVERT: B 462 MET cc_start: 0.8215 (mtm) cc_final: 0.7813 (mtp) REVERT: B 496 MET cc_start: 0.8688 (mtp) cc_final: 0.8450 (mtt) REVERT: B 520 GLU cc_start: 0.8318 (mp0) cc_final: 0.7558 (mp0) REVERT: B 547 MET cc_start: 0.9016 (tpp) cc_final: 0.8696 (ttm) REVERT: B 574 MET cc_start: 0.7355 (tpp) cc_final: 0.7007 (tpp) REVERT: B 587 LYS cc_start: 0.8251 (mmtm) cc_final: 0.8011 (mmmt) REVERT: B 616 LEU cc_start: 0.8584 (mt) cc_final: 0.8351 (mm) REVERT: B 629 ARG cc_start: 0.8020 (mpp-170) cc_final: 0.7276 (mtm180) REVERT: B 663 ARG cc_start: 0.6601 (tpp-160) cc_final: 0.5281 (tmt170) REVERT: B 681 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 10 GLU cc_start: 0.9152 (mp0) cc_final: 0.8734 (mp0) REVERT: C 22 LYS cc_start: 0.7047 (mmpt) cc_final: 0.6734 (mmpt) REVERT: C 51 MET cc_start: 0.8951 (tpp) cc_final: 0.8482 (tpp) REVERT: C 55 MET cc_start: 0.8458 (mmm) cc_final: 0.8169 (mmm) REVERT: C 85 LYS cc_start: 0.6235 (mmtm) cc_final: 0.5869 (mmmm) REVERT: C 102 ILE cc_start: 0.9148 (mt) cc_final: 0.8893 (mp) REVERT: C 103 THR cc_start: 0.9246 (p) cc_final: 0.8904 (t) REVERT: C 155 GLN cc_start: 0.8318 (tp40) cc_final: 0.8016 (tp40) REVERT: C 213 MET cc_start: 0.9076 (ptm) cc_final: 0.8719 (ppp) REVERT: C 218 PHE cc_start: 0.8467 (m-10) cc_final: 0.7467 (m-80) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2603 time to fit residues: 130.9805 Evaluate side-chains 302 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 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 = 0.3738 r_free = 0.3738 target = 0.127851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105485 restraints weight = 28151.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108544 restraints weight = 16416.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110679 restraints weight = 11063.825| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12545 Z= 0.140 Angle : 0.629 10.537 16962 Z= 0.318 Chirality : 0.042 0.154 1855 Planarity : 0.004 0.059 2070 Dihedral : 11.181 73.640 1924 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1441 helix: 0.65 (0.21), residues: 658 sheet: -1.22 (0.52), residues: 100 loop : -2.29 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 83 HIS 0.004 0.001 HIS C 216 PHE 0.020 0.001 PHE B 108 TYR 0.031 0.002 TYR B 736 ARG 0.016 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 531) hydrogen bonds : angle 4.41068 ( 1457) covalent geometry : bond 0.00317 (12545) covalent geometry : angle 0.62928 (16962) *********************** 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 344 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.319 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 332 GLU cc_start: 0.7181 (pt0) cc_final: 0.6853 (pm20) REVERT: A 340 ASP cc_start: 0.8729 (t0) cc_final: 0.8455 (t70) REVERT: A 453 GLU cc_start: 0.8183 (tp30) cc_final: 0.7877 (tp30) REVERT: A 633 TYR cc_start: 0.8617 (m-80) cc_final: 0.8260 (m-80) REVERT: A 639 ASP cc_start: 0.7923 (t70) cc_final: 0.7703 (t0) REVERT: A 643 GLU cc_start: 0.8532 (pm20) cc_final: 0.8213 (mp0) REVERT: A 684 ASN cc_start: 0.9259 (t0) cc_final: 0.8553 (m110) REVERT: B 2 GLU cc_start: 0.6603 (mt-10) cc_final: 0.5785 (mp0) REVERT: B 4 ASN cc_start: 0.9304 (t0) cc_final: 0.8873 (t0) REVERT: B 80 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9079 (mmtm) REVERT: B 87 ILE cc_start: 0.9208 (pt) cc_final: 0.8886 (pt) REVERT: B 112 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8358 (mp0) REVERT: B 120 MET cc_start: 0.5912 (ppp) cc_final: 0.5395 (ppp) REVERT: B 133 ASP cc_start: 0.8300 (t70) cc_final: 0.8053 (m-30) REVERT: B 155 GLU cc_start: 0.7775 (pp20) cc_final: 0.7545 (pp20) REVERT: B 174 GLU cc_start: 0.8789 (tt0) cc_final: 0.8111 (tm-30) REVERT: B 237 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8792 (mptt) REVERT: B 250 ILE cc_start: 0.8855 (mp) cc_final: 0.8644 (mp) REVERT: B 312 ASN cc_start: 0.8970 (m110) cc_final: 0.8234 (m-40) REVERT: B 320 TYR cc_start: 0.8050 (m-10) cc_final: 0.7625 (m-10) REVERT: B 336 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8525 (mttp) REVERT: B 370 ILE cc_start: 0.9046 (mm) cc_final: 0.8518 (tp) REVERT: B 383 ASN cc_start: 0.8559 (m-40) cc_final: 0.8346 (m110) REVERT: B 397 MET cc_start: 0.7814 (tpp) cc_final: 0.7392 (tpp) REVERT: B 402 CYS cc_start: 0.8278 (t) cc_final: 0.7951 (t) REVERT: B 408 MET cc_start: 0.8093 (ttm) cc_final: 0.7626 (ttp) REVERT: B 462 MET cc_start: 0.8176 (mtm) cc_final: 0.7899 (mtp) REVERT: B 520 GLU cc_start: 0.8322 (mp0) cc_final: 0.7692 (mp0) REVERT: B 547 MET cc_start: 0.8882 (tpp) cc_final: 0.8549 (ttm) REVERT: B 574 MET cc_start: 0.7379 (tpp) cc_final: 0.7006 (tpp) REVERT: B 587 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7987 (mmmt) REVERT: B 629 ARG cc_start: 0.7870 (mpp-170) cc_final: 0.7284 (mtm180) REVERT: B 681 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7515 (mm-30) REVERT: C 22 LYS cc_start: 0.6860 (mmpt) cc_final: 0.6479 (mmpt) REVERT: C 51 MET cc_start: 0.8922 (tpp) cc_final: 0.8551 (tpp) REVERT: C 55 MET cc_start: 0.8570 (mmm) cc_final: 0.8200 (mmm) REVERT: C 85 LYS cc_start: 0.6436 (mmtm) cc_final: 0.6035 (mmmm) REVERT: C 102 ILE cc_start: 0.9158 (mt) cc_final: 0.8901 (mp) REVERT: C 103 THR cc_start: 0.9204 (p) cc_final: 0.8855 (t) REVERT: C 155 GLN cc_start: 0.8392 (tp40) cc_final: 0.8059 (tp40) REVERT: C 213 MET cc_start: 0.9133 (ptm) cc_final: 0.8722 (ppp) REVERT: C 218 PHE cc_start: 0.8515 (m-10) cc_final: 0.8282 (m-10) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2466 time to fit residues: 120.4576 Evaluate side-chains 289 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 0.0770 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 0.0000 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107315 restraints weight = 28170.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110477 restraints weight = 16439.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112673 restraints weight = 11030.687| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6088 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= 0.119 Angle : 0.624 9.120 16962 Z= 0.315 Chirality : 0.041 0.148 1855 Planarity : 0.004 0.051 2070 Dihedral : 11.119 73.467 1924 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1441 helix: 0.80 (0.21), residues: 652 sheet: -1.31 (0.52), residues: 100 loop : -2.23 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 83 HIS 0.004 0.001 HIS C 216 PHE 0.019 0.001 PHE A 292 TYR 0.024 0.001 TYR B 736 ARG 0.014 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 531) hydrogen bonds : angle 4.33085 ( 1457) covalent geometry : bond 0.00270 (12545) covalent geometry : angle 0.62377 (16962) *********************** 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 343 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.383 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 188 TYR cc_start: 0.8924 (t80) cc_final: 0.8717 (t80) REVERT: A 193 PHE cc_start: 0.9135 (t80) cc_final: 0.8748 (t80) REVERT: A 235 ARG cc_start: 0.6958 (tpm170) cc_final: 0.6679 (mmm160) REVERT: A 252 GLU cc_start: 0.7976 (tp30) cc_final: 0.7768 (tp30) REVERT: A 340 ASP cc_start: 0.8704 (t0) cc_final: 0.8417 (t70) REVERT: A 453 GLU cc_start: 0.8154 (tp30) cc_final: 0.7769 (tp30) REVERT: A 457 PHE cc_start: 0.8703 (m-80) cc_final: 0.7671 (m-80) REVERT: A 493 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7943 (ttpt) REVERT: A 549 TYR cc_start: 0.8046 (m-10) cc_final: 0.7843 (m-10) REVERT: A 633 TYR cc_start: 0.8598 (m-80) cc_final: 0.8350 (m-80) REVERT: A 650 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8408 (ptpt) REVERT: A 684 ASN cc_start: 0.9151 (t0) cc_final: 0.8853 (t0) REVERT: B 78 LEU cc_start: 0.8827 (tp) cc_final: 0.8617 (tt) REVERT: B 80 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9093 (mmtm) REVERT: B 133 ASP cc_start: 0.8397 (t70) cc_final: 0.7915 (m-30) REVERT: B 174 GLU cc_start: 0.8651 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 312 ASN cc_start: 0.8951 (m110) cc_final: 0.8155 (m-40) REVERT: B 320 TYR cc_start: 0.7975 (m-10) cc_final: 0.7566 (m-10) REVERT: B 336 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8544 (mttp) REVERT: B 370 ILE cc_start: 0.9019 (mm) cc_final: 0.8516 (tp) REVERT: B 408 MET cc_start: 0.8090 (ttm) cc_final: 0.7677 (ttp) REVERT: B 453 ILE cc_start: 0.8979 (pt) cc_final: 0.8404 (tp) REVERT: B 520 GLU cc_start: 0.8454 (mp0) cc_final: 0.7707 (mp0) REVERT: B 574 MET cc_start: 0.7243 (tpp) cc_final: 0.7019 (tpp) REVERT: B 587 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7976 (mmmt) REVERT: B 599 MET cc_start: 0.8483 (tpp) cc_final: 0.8176 (tpt) REVERT: B 629 ARG cc_start: 0.7845 (mpp-170) cc_final: 0.7280 (mtm180) REVERT: B 681 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 51 MET cc_start: 0.8869 (tpp) cc_final: 0.8552 (tpp) REVERT: C 55 MET cc_start: 0.8570 (mmm) cc_final: 0.8204 (mmm) REVERT: C 85 LYS cc_start: 0.6435 (mmtm) cc_final: 0.6015 (mmmm) REVERT: C 102 ILE cc_start: 0.9153 (mt) cc_final: 0.8902 (mp) REVERT: C 103 THR cc_start: 0.9214 (p) cc_final: 0.8860 (t) REVERT: C 155 GLN cc_start: 0.8307 (tp40) cc_final: 0.7934 (tp40) REVERT: C 213 MET cc_start: 0.9151 (ptm) cc_final: 0.8731 (ppp) REVERT: C 218 PHE cc_start: 0.8492 (m-10) cc_final: 0.8285 (m-10) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2597 time to fit residues: 126.9642 Evaluate side-chains 285 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 5.9990 chunk 143 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106459 restraints weight = 27704.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109572 restraints weight = 15998.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111703 restraints weight = 10649.491| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12545 Z= 0.132 Angle : 0.638 9.610 16962 Z= 0.324 Chirality : 0.042 0.178 1855 Planarity : 0.004 0.054 2070 Dihedral : 11.126 73.488 1924 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1441 helix: 0.74 (0.21), residues: 650 sheet: -1.19 (0.52), residues: 100 loop : -2.25 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 38 HIS 0.005 0.001 HIS C 216 PHE 0.020 0.002 PHE C 212 TYR 0.021 0.002 TYR A 208 ARG 0.013 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 531) hydrogen bonds : angle 4.42163 ( 1457) covalent geometry : bond 0.00300 (12545) covalent geometry : angle 0.63816 (16962) ********************** 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 331 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.722 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: 0.9033 (t80) cc_final: 0.8734 (t80) REVERT: A 340 ASP cc_start: 0.8685 (t0) cc_final: 0.8427 (t70) REVERT: A 453 GLU cc_start: 0.8105 (tp30) cc_final: 0.7732 (tp30) REVERT: A 457 PHE cc_start: 0.8698 (m-80) cc_final: 0.7670 (m-80) REVERT: A 493 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7837 (ttpt) REVERT: A 633 TYR cc_start: 0.8635 (m-80) cc_final: 0.8336 (m-80) REVERT: A 684 ASN cc_start: 0.9214 (t0) cc_final: 0.8921 (t0) REVERT: A 709 PHE cc_start: 0.7077 (t80) cc_final: 0.6734 (t80) REVERT: B 1 MET cc_start: 0.7728 (tmm) cc_final: 0.7522 (tmm) REVERT: B 4 ASN cc_start: 0.9184 (t0) cc_final: 0.8723 (t0) REVERT: B 6 TYR cc_start: 0.8669 (m-80) cc_final: 0.8400 (m-80) REVERT: B 7 LEU cc_start: 0.9530 (mt) cc_final: 0.9182 (mt) REVERT: B 80 LYS cc_start: 0.9305 (mmmm) cc_final: 0.9055 (mmtm) REVERT: B 85 VAL cc_start: 0.9123 (t) cc_final: 0.8882 (t) REVERT: B 147 GLN cc_start: 0.8566 (tp40) cc_final: 0.8353 (tm-30) REVERT: B 174 GLU cc_start: 0.8674 (tt0) cc_final: 0.7718 (tm-30) REVERT: B 178 TRP cc_start: 0.7617 (m-10) cc_final: 0.6828 (m-10) REVERT: B 250 ILE cc_start: 0.8838 (mp) cc_final: 0.8633 (mp) REVERT: B 312 ASN cc_start: 0.8950 (m110) cc_final: 0.8199 (m-40) REVERT: B 320 TYR cc_start: 0.7947 (m-10) cc_final: 0.7679 (m-10) REVERT: B 336 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8694 (ptpt) REVERT: B 370 ILE cc_start: 0.9044 (mm) cc_final: 0.8519 (tp) REVERT: B 383 ASN cc_start: 0.8591 (m-40) cc_final: 0.8352 (m110) REVERT: B 402 CYS cc_start: 0.8291 (t) cc_final: 0.7990 (t) REVERT: B 408 MET cc_start: 0.8069 (ttm) cc_final: 0.7655 (ttp) REVERT: B 520 GLU cc_start: 0.8431 (mp0) cc_final: 0.7738 (mp0) REVERT: B 547 MET cc_start: 0.8852 (tpp) cc_final: 0.8499 (ttm) REVERT: B 574 MET cc_start: 0.7247 (tpp) cc_final: 0.7029 (tpp) REVERT: B 587 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7945 (mmmt) REVERT: B 629 ARG cc_start: 0.7877 (mpp-170) cc_final: 0.7290 (mtm180) REVERT: B 663 ARG cc_start: 0.6600 (tpp-160) cc_final: 0.5354 (tmt170) REVERT: B 681 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7532 (tt0) REVERT: B 740 LYS cc_start: 0.9004 (mttt) cc_final: 0.8680 (mmtt) REVERT: C 32 TYR cc_start: 0.8210 (t80) cc_final: 0.7859 (t80) REVERT: C 51 MET cc_start: 0.8856 (tpp) cc_final: 0.8605 (tpp) REVERT: C 55 MET cc_start: 0.8620 (mmm) cc_final: 0.8386 (mmm) REVERT: C 85 LYS cc_start: 0.6397 (mmtm) cc_final: 0.5989 (mmmm) REVERT: C 102 ILE cc_start: 0.9160 (mt) cc_final: 0.8913 (mp) REVERT: C 103 THR cc_start: 0.9203 (p) cc_final: 0.8865 (t) REVERT: C 155 GLN cc_start: 0.8136 (tp40) cc_final: 0.7788 (tp40) REVERT: C 200 TYR cc_start: 0.6878 (m-80) cc_final: 0.6578 (m-80) REVERT: C 218 PHE cc_start: 0.8435 (m-10) cc_final: 0.8215 (m-10) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.3039 time to fit residues: 146.1663 Evaluate side-chains 284 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 145 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105033 restraints weight = 27881.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108229 restraints weight = 16333.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110415 restraints weight = 11014.773| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6373 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= 0.145 Angle : 0.653 9.318 16962 Z= 0.331 Chirality : 0.043 0.145 1855 Planarity : 0.005 0.056 2070 Dihedral : 11.127 73.507 1924 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1441 helix: 0.71 (0.21), residues: 653 sheet: -1.07 (0.54), residues: 96 loop : -2.18 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 38 HIS 0.003 0.001 HIS A 451 PHE 0.018 0.001 PHE B 451 TYR 0.022 0.002 TYR B 6 ARG 0.014 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 531) hydrogen bonds : angle 4.47140 ( 1457) covalent geometry : bond 0.00330 (12545) covalent geometry : angle 0.65269 (16962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.64 seconds wall clock time: 93 minutes 11.41 seconds (5591.41 seconds total)