Starting phenix.real_space_refine on Wed Jul 30 16:57:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581.map" model { file = "/net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kur_9581/07_2025/6kur_9581_neut.cif" } resolution = 3.7 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= 0.011 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 28 5.49 5 S 109 5.16 5 C 7765 2.51 5 N 2113 2.21 5 O 2369 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: 12384 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: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5603 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 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: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 9} 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: 6.98, per 1000 atoms: 0.56 Number of scatterers: 12384 At special positions: 0 Unit cell: (110.16, 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 28 15.00 O 2369 8.00 N 2113 7.00 C 7765 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 47.2% alpha, 7.7% beta 7 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.700A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.500A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.118A 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 296 through 300 removed outlier: 3.719A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) 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 removed outlier: 3.645A pdb=" N GLU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.704A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 620 through 637 removed outlier: 4.119A pdb=" N CYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.623A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.734A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.676A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.513A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (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 164 through 177 removed outlier: 3.584A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.672A 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: 3.570A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.788A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.666A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.573A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.832A 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 392 removed outlier: 3.847A pdb=" N THR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.501A 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 removed outlier: 3.568A pdb=" N ALA B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.691A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.682A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.721A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.800A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.654A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.646A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.942A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.772A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.612A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.690A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.616A 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: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.621A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.875A 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: 3.624A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.349A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.774A 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 601 through 604 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.502A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.481A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.679A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.745A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153 496 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2031 1.32 - 1.44: 3402 1.44 - 1.57: 7019 1.57 - 1.69: 54 1.69 - 1.82: 181 Bond restraints: 12687 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.376 -0.043 8.40e-03 1.42e+04 2.61e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.89e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.27e-02 6.20e+03 1.84e+01 bond pdb=" C PHE A 563 " pdb=" O PHE A 563 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.43e-02 4.89e+03 7.32e+00 bond pdb=" N ILE A 571 " pdb=" CA ILE A 571 " ideal model delta sigma weight residual 1.461 1.430 0.031 1.23e-02 6.61e+03 6.55e+00 ... (remaining 12682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 16858 2.51 - 5.02: 277 5.02 - 7.53: 37 7.53 - 10.04: 7 10.04 - 12.55: 1 Bond angle restraints: 17180 Sorted by residual: angle pdb=" C4' U R 9 " pdb=" C3' U R 9 " pdb=" O3' U R 9 " ideal model delta sigma weight residual 109.40 121.95 -12.55 1.50e+00 4.44e-01 7.00e+01 angle pdb=" N ASN A 560 " pdb=" CA ASN A 560 " pdb=" C ASN A 560 " ideal model delta sigma weight residual 113.55 105.32 8.23 1.26e+00 6.30e-01 4.27e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 112.93 104.68 8.25 1.33e+00 5.65e-01 3.85e+01 angle pdb=" N MET A 574 " pdb=" CA MET A 574 " pdb=" C MET A 574 " ideal model delta sigma weight residual 111.69 105.79 5.90 1.23e+00 6.61e-01 2.30e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.66 -5.09 1.25e+00 6.40e-01 1.66e+01 ... (remaining 17175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 7685 35.18 - 70.36: 118 70.36 - 105.53: 12 105.53 - 140.71: 1 140.71 - 175.89: 1 Dihedral angle restraints: 7817 sinusoidal: 3545 harmonic: 4272 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 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+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 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE A 604 " pdb=" C ILE A 604 " pdb=" N ALA A 605 " pdb=" CA ALA A 605 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1808 0.112 - 0.224: 73 0.224 - 0.336: 4 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C3' U R 9 " pdb=" C4' U R 9 " pdb=" O3' U R 9 " pdb=" C2' U R 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.84e+00 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 2.35 0.29 2.00e-01 2.50e+01 2.10e+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 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1883 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE A 628 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 425 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C GLU A 425 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 425 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 426 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 424 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C CYS A 424 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS A 424 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 425 " -0.017 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 316 2.69 - 3.25: 11111 3.25 - 3.80: 17979 3.80 - 4.35: 24423 4.35 - 4.90: 40297 Nonbonded interactions: 94126 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.143 3.120 nonbonded pdb=" OD2 ASP B 523 " pdb=" OH TYR B 560 " model vdw 2.248 3.040 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.251 3.120 nonbonded pdb=" O2' U R 8 " pdb=" OP1 U R 9 " model vdw 2.258 3.040 nonbonded pdb=" O LYS A 460 " pdb=" NZ LYS A 486 " model vdw 2.278 3.120 ... (remaining 94121 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: 0.270 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.160 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 0.055 12687 Z= 0.227 Angle : 0.788 12.553 17180 Z= 0.445 Chirality : 0.052 0.560 1886 Planarity : 0.006 0.062 2080 Dihedral : 12.356 175.889 5043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.99 % Favored : 92.87 % Rotamer: Outliers : 1.01 % Allowed : 2.41 % Favored : 96.58 % 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: -4.96 (0.16), residues: 1445 helix: -3.55 (0.11), residues: 642 sheet: -1.69 (0.48), residues: 122 loop : -3.30 (0.19), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 386 HIS 0.009 0.002 HIS A 451 PHE 0.023 0.002 PHE B 420 TYR 0.020 0.002 TYR B 38 ARG 0.008 0.001 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.14893 ( 515) hydrogen bonds : angle 9.24728 ( 1430) covalent geometry : bond 0.00403 (12687) covalent geometry : angle 0.78774 (17180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 491 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ASN cc_start: 0.8232 (t0) cc_final: 0.7712 (t0) REVERT: A 516 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 558 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (tm) REVERT: A 568 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8695 (ptt90) REVERT: A 653 LEU cc_start: 0.9177 (mp) cc_final: 0.8890 (mt) REVERT: A 702 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7689 (tttp) REVERT: B 71 THR cc_start: 0.8139 (p) cc_final: 0.7856 (p) REVERT: B 226 ILE cc_start: 0.9133 (mt) cc_final: 0.8875 (pt) REVERT: B 388 ASP cc_start: 0.7501 (m-30) cc_final: 0.7187 (m-30) REVERT: B 554 GLN cc_start: 0.8937 (tp40) cc_final: 0.8584 (tp-100) REVERT: B 675 MET cc_start: 0.5670 (mmm) cc_final: 0.5241 (mmt) REVERT: B 705 ILE cc_start: 0.8832 (pt) cc_final: 0.8609 (mt) REVERT: B 730 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6597 (mm) REVERT: B 736 TYR cc_start: 0.8314 (t80) cc_final: 0.7757 (t80) REVERT: C 180 ASN cc_start: 0.4069 (t0) cc_final: 0.3837 (m-40) REVERT: C 205 VAL cc_start: 0.8948 (t) cc_final: 0.8647 (p) REVERT: C 235 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7727 (ptm-80) outliers start: 13 outliers final: 4 residues processed: 501 average time/residue: 0.3275 time to fit residues: 219.2160 Evaluate side-chains 297 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 290 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 133 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 638 ASN A 640 ASN A 657 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 157 GLN B 299 GLN B 315 GLN B 436 ASN B 477 ASN B 563 HIS B 572 HIS C 141 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111593 restraints weight = 18935.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115106 restraints weight = 9890.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117443 restraints weight = 6432.710| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12687 Z= 0.232 Angle : 0.688 11.217 17180 Z= 0.358 Chirality : 0.045 0.157 1886 Planarity : 0.005 0.055 2080 Dihedral : 13.759 170.098 2027 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 3.88 % Allowed : 12.97 % Favored : 83.15 % 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: 1445 helix: -1.18 (0.18), residues: 663 sheet: -0.86 (0.51), residues: 128 loop : -3.07 (0.20), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 386 HIS 0.008 0.002 HIS A 451 PHE 0.021 0.002 PHE B 108 TYR 0.013 0.002 TYR B 350 ARG 0.005 0.001 ARG B 741 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 515) hydrogen bonds : angle 5.30866 ( 1430) covalent geometry : bond 0.00527 (12687) covalent geometry : angle 0.68764 (17180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8229 (tmm) cc_final: 0.7703 (ttm) REVERT: A 382 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: A 387 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8929 (mm) REVERT: A 426 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 427 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 502 THR cc_start: 0.8558 (p) cc_final: 0.8264 (p) REVERT: A 504 GLU cc_start: 0.7819 (mp0) cc_final: 0.7371 (mp0) REVERT: A 558 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8563 (tm) REVERT: A 568 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8802 (ptt90) REVERT: A 702 LYS cc_start: 0.8356 (tmtt) cc_final: 0.8045 (tttp) REVERT: B 71 THR cc_start: 0.8451 (p) cc_final: 0.8210 (p) REVERT: B 93 LEU cc_start: 0.9215 (mt) cc_final: 0.8987 (tp) REVERT: B 140 MET cc_start: 0.7565 (mtt) cc_final: 0.7351 (mtp) REVERT: B 147 GLN cc_start: 0.8919 (tp40) cc_final: 0.8719 (mm110) REVERT: B 210 MET cc_start: 0.5571 (ptt) cc_final: 0.5297 (ptp) REVERT: B 222 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8465 (ttm170) REVERT: B 266 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 289 SER cc_start: 0.9039 (m) cc_final: 0.8567 (p) REVERT: B 388 ASP cc_start: 0.8226 (m-30) cc_final: 0.7973 (m-30) REVERT: B 423 MET cc_start: 0.8607 (mtm) cc_final: 0.8115 (mtm) REVERT: B 442 LEU cc_start: 0.8970 (tp) cc_final: 0.8566 (mt) REVERT: B 523 ASP cc_start: 0.8246 (m-30) cc_final: 0.7764 (m-30) REVERT: B 675 MET cc_start: 0.4926 (mmm) cc_final: 0.4411 (mmt) REVERT: B 705 ILE cc_start: 0.8999 (pt) cc_final: 0.8694 (mt) REVERT: C 234 GLU cc_start: 0.7491 (pm20) cc_final: 0.7221 (pp20) REVERT: C 235 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8291 (ptt90) outliers start: 50 outliers final: 28 residues processed: 310 average time/residue: 0.2972 time to fit residues: 131.8144 Evaluate side-chains 271 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 436 ASN B 660 HIS C 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111080 restraints weight = 19259.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114682 restraints weight = 9937.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116975 restraints weight = 6432.948| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12687 Z= 0.135 Angle : 0.585 10.298 17180 Z= 0.299 Chirality : 0.042 0.148 1886 Planarity : 0.004 0.052 2080 Dihedral : 13.442 170.430 2014 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.34 % Allowed : 15.45 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.21), residues: 1445 helix: -0.23 (0.20), residues: 666 sheet: -0.35 (0.56), residues: 110 loop : -2.91 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 388 HIS 0.004 0.001 HIS A 451 PHE 0.017 0.001 PHE A 632 TYR 0.012 0.001 TYR B 736 ARG 0.007 0.001 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 515) hydrogen bonds : angle 4.68901 ( 1430) covalent geometry : bond 0.00301 (12687) covalent geometry : angle 0.58472 (17180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: A 382 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 425 GLU cc_start: 0.8254 (tp30) cc_final: 0.7828 (mm-30) REVERT: A 426 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 427 LEU cc_start: 0.8949 (tt) cc_final: 0.8693 (tt) REVERT: A 504 GLU cc_start: 0.7858 (mp0) cc_final: 0.7500 (mp0) REVERT: A 633 TYR cc_start: 0.9452 (m-10) cc_final: 0.9210 (m-80) REVERT: A 702 LYS cc_start: 0.8280 (tmtt) cc_final: 0.8004 (ttpt) REVERT: B 41 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 45 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7719 (ttp-170) REVERT: B 71 THR cc_start: 0.8342 (p) cc_final: 0.8067 (p) REVERT: B 140 MET cc_start: 0.7400 (mtt) cc_final: 0.7154 (mtp) REVERT: B 266 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 289 SER cc_start: 0.9006 (m) cc_final: 0.8523 (p) REVERT: B 388 ASP cc_start: 0.8194 (m-30) cc_final: 0.7930 (m-30) REVERT: B 423 MET cc_start: 0.8626 (mtm) cc_final: 0.8235 (mtm) REVERT: B 442 LEU cc_start: 0.8841 (tp) cc_final: 0.8507 (mt) REVERT: B 474 MET cc_start: 0.8429 (ttm) cc_final: 0.8202 (mtp) REVERT: B 489 GLU cc_start: 0.6859 (pm20) cc_final: 0.6561 (pm20) REVERT: B 523 ASP cc_start: 0.8083 (m-30) cc_final: 0.7575 (m-30) REVERT: B 578 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8161 (mtp85) REVERT: B 615 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: B 705 ILE cc_start: 0.8918 (pt) cc_final: 0.8686 (mt) REVERT: B 738 GLU cc_start: 0.8151 (tt0) cc_final: 0.7943 (mt-10) REVERT: C 164 LYS cc_start: 0.9086 (tppt) cc_final: 0.8653 (tppt) REVERT: C 217 GLN cc_start: 0.7924 (tt0) cc_final: 0.7619 (mt0) REVERT: C 218 PHE cc_start: 0.8281 (m-10) cc_final: 0.7837 (m-80) REVERT: C 235 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8113 (ptt90) outliers start: 43 outliers final: 27 residues processed: 290 average time/residue: 0.3489 time to fit residues: 149.5704 Evaluate side-chains 269 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 725 GLN C 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110725 restraints weight = 19244.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114300 restraints weight = 9945.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116598 restraints weight = 6439.074| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12687 Z= 0.136 Angle : 0.590 10.324 17180 Z= 0.300 Chirality : 0.042 0.152 1886 Planarity : 0.004 0.048 2080 Dihedral : 13.265 169.821 2008 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.26 % Allowed : 16.23 % Favored : 80.51 % 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: -1.65 (0.21), residues: 1445 helix: 0.25 (0.20), residues: 663 sheet: -0.05 (0.59), residues: 100 loop : -2.74 (0.20), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 386 HIS 0.005 0.001 HIS A 451 PHE 0.015 0.001 PHE A 632 TYR 0.010 0.001 TYR B 736 ARG 0.006 0.000 ARG B 741 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 515) hydrogen bonds : angle 4.48216 ( 1430) covalent geometry : bond 0.00304 (12687) covalent geometry : angle 0.59010 (17180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8297 (tmm) cc_final: 0.7674 (tmm) REVERT: A 382 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: A 387 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8808 (mm) REVERT: A 425 GLU cc_start: 0.8124 (tp30) cc_final: 0.7742 (mm-30) REVERT: A 426 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 427 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 626 MET cc_start: 0.7724 (ttt) cc_final: 0.7370 (ttt) REVERT: A 654 MET cc_start: 0.9044 (tpp) cc_final: 0.8801 (tpp) REVERT: A 702 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8060 (ttpt) REVERT: B 1 MET cc_start: 0.7344 (tmm) cc_final: 0.7117 (tmm) REVERT: B 41 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6911 (tm-30) REVERT: B 71 THR cc_start: 0.8309 (p) cc_final: 0.8026 (p) REVERT: B 93 LEU cc_start: 0.9154 (tt) cc_final: 0.8934 (tt) REVERT: B 140 MET cc_start: 0.7348 (mtt) cc_final: 0.7095 (mtp) REVERT: B 147 GLN cc_start: 0.8474 (mm110) cc_final: 0.8159 (mm110) REVERT: B 148 LEU cc_start: 0.9168 (mp) cc_final: 0.8864 (mp) REVERT: B 222 ARG cc_start: 0.8649 (ttm170) cc_final: 0.7957 (ttt180) REVERT: B 289 SER cc_start: 0.9005 (m) cc_final: 0.8520 (p) REVERT: B 388 ASP cc_start: 0.8212 (m-30) cc_final: 0.7940 (m-30) REVERT: B 523 ASP cc_start: 0.7994 (m-30) cc_final: 0.7509 (m-30) REVERT: B 615 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: B 705 ILE cc_start: 0.8914 (pt) cc_final: 0.8710 (mt) REVERT: B 730 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6179 (pt) REVERT: C 218 PHE cc_start: 0.8309 (m-10) cc_final: 0.8036 (m-80) REVERT: C 235 ARG cc_start: 0.8314 (ptm-80) cc_final: 0.7943 (ptt90) outliers start: 42 outliers final: 27 residues processed: 275 average time/residue: 0.4212 time to fit residues: 170.4932 Evaluate side-chains 261 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111676 restraints weight = 19337.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115095 restraints weight = 10073.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117351 restraints weight = 6559.747| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12687 Z= 0.131 Angle : 0.581 9.726 17180 Z= 0.296 Chirality : 0.042 0.158 1886 Planarity : 0.004 0.047 2080 Dihedral : 13.198 168.848 2008 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.57 % Allowed : 16.38 % Favored : 80.05 % 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: -1.39 (0.21), residues: 1445 helix: 0.47 (0.20), residues: 665 sheet: 0.06 (0.58), residues: 100 loop : -2.62 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 132 HIS 0.005 0.001 HIS A 451 PHE 0.016 0.001 PHE C 212 TYR 0.008 0.001 TYR B 736 ARG 0.009 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 515) hydrogen bonds : angle 4.34317 ( 1430) covalent geometry : bond 0.00296 (12687) covalent geometry : angle 0.58067 (17180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: A 387 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8731 (mm) REVERT: A 425 GLU cc_start: 0.8114 (tp30) cc_final: 0.7739 (mm-30) REVERT: A 426 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 427 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 654 MET cc_start: 0.8970 (tpp) cc_final: 0.8719 (tpp) REVERT: A 702 LYS cc_start: 0.8350 (tmtt) cc_final: 0.8078 (ttpt) REVERT: B 41 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 71 THR cc_start: 0.8358 (p) cc_final: 0.8061 (p) REVERT: B 147 GLN cc_start: 0.8420 (mm110) cc_final: 0.8149 (mm110) REVERT: B 148 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 248 MET cc_start: 0.7441 (tpp) cc_final: 0.7081 (tpp) REVERT: B 266 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 388 ASP cc_start: 0.8164 (m-30) cc_final: 0.7887 (m-30) REVERT: B 523 ASP cc_start: 0.8082 (m-30) cc_final: 0.7616 (m-30) REVERT: B 578 ARG cc_start: 0.8667 (ttm110) cc_final: 0.8206 (mtp85) REVERT: C 44 GLU cc_start: 0.6594 (tp30) cc_final: 0.6360 (tp30) REVERT: C 74 PRO cc_start: 0.7625 (Cg_exo) cc_final: 0.7425 (Cg_endo) REVERT: C 174 LEU cc_start: 0.7767 (mm) cc_final: 0.7541 (mm) REVERT: C 176 GLU cc_start: 0.7891 (mp0) cc_final: 0.7593 (pm20) REVERT: C 234 GLU cc_start: 0.7922 (pm20) cc_final: 0.7291 (pp20) outliers start: 46 outliers final: 29 residues processed: 274 average time/residue: 0.2525 time to fit residues: 99.0952 Evaluate side-chains 258 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 129 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 299 GLN B 436 ASN C 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111090 restraints weight = 19569.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114667 restraints weight = 10102.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117032 restraints weight = 6578.824| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12687 Z= 0.112 Angle : 0.577 8.311 17180 Z= 0.292 Chirality : 0.041 0.154 1886 Planarity : 0.004 0.048 2080 Dihedral : 13.065 167.587 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 3.34 % Allowed : 17.08 % Favored : 79.58 % 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: 1445 helix: 0.64 (0.20), residues: 663 sheet: 0.09 (0.58), residues: 100 loop : -2.53 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.021 0.001 PHE B 108 TYR 0.009 0.001 TYR B 560 ARG 0.007 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 515) hydrogen bonds : angle 4.18741 ( 1430) covalent geometry : bond 0.00247 (12687) covalent geometry : angle 0.57663 (17180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7386 (ttm) cc_final: 0.6849 (ttm) REVERT: A 196 MET cc_start: 0.8262 (tmm) cc_final: 0.7671 (tmm) REVERT: A 382 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: A 387 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 425 GLU cc_start: 0.8093 (tp30) cc_final: 0.7734 (mm-30) REVERT: A 426 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 427 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 654 MET cc_start: 0.8923 (tpp) cc_final: 0.8673 (tpp) REVERT: A 702 LYS cc_start: 0.8360 (tmtt) cc_final: 0.8054 (ttpt) REVERT: B 41 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7025 (tm-30) REVERT: B 71 THR cc_start: 0.8338 (p) cc_final: 0.8044 (p) REVERT: B 147 GLN cc_start: 0.8336 (mm110) cc_final: 0.8091 (mm110) REVERT: B 148 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 222 ARG cc_start: 0.8537 (ttm170) cc_final: 0.7841 (ttt180) REVERT: B 248 MET cc_start: 0.7591 (tpp) cc_final: 0.7227 (tpp) REVERT: B 266 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 388 ASP cc_start: 0.8200 (m-30) cc_final: 0.7935 (m-30) REVERT: B 523 ASP cc_start: 0.8025 (m-30) cc_final: 0.7553 (m-30) REVERT: B 578 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8238 (mtp85) REVERT: B 615 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: B 748 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7758 (mmm160) REVERT: C 38 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7502 (m100) REVERT: C 74 PRO cc_start: 0.7717 (Cg_exo) cc_final: 0.7510 (Cg_endo) REVERT: C 176 GLU cc_start: 0.7957 (mp0) cc_final: 0.7627 (pm20) REVERT: C 234 GLU cc_start: 0.7788 (pm20) cc_final: 0.7198 (pp20) outliers start: 43 outliers final: 27 residues processed: 267 average time/residue: 0.2496 time to fit residues: 95.8092 Evaluate side-chains 264 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 56 optimal weight: 0.0060 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115242 restraints weight = 19286.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118769 restraints weight = 10030.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121091 restraints weight = 6511.792| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12687 Z= 0.104 Angle : 0.584 8.920 17180 Z= 0.294 Chirality : 0.041 0.149 1886 Planarity : 0.004 0.047 2080 Dihedral : 13.012 166.148 2006 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 3.26 % Allowed : 17.70 % Favored : 79.04 % 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: -1.01 (0.22), residues: 1445 helix: 0.79 (0.20), residues: 662 sheet: -0.16 (0.52), residues: 120 loop : -2.40 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.017 0.001 PHE B 108 TYR 0.010 0.001 TYR B 560 ARG 0.005 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 515) hydrogen bonds : angle 4.08139 ( 1430) covalent geometry : bond 0.00225 (12687) covalent geometry : angle 0.58418 (17180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6834 (ttm) REVERT: A 196 MET cc_start: 0.8316 (tmm) cc_final: 0.7666 (tmm) REVERT: A 221 ASN cc_start: 0.8422 (t0) cc_final: 0.8078 (t0) REVERT: A 222 GLN cc_start: 0.7989 (mm110) cc_final: 0.7321 (mm-40) REVERT: A 382 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: A 387 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 425 GLU cc_start: 0.8001 (tp30) cc_final: 0.7757 (mm-30) REVERT: A 426 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 427 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 442 LYS cc_start: 0.9023 (tttt) cc_final: 0.8469 (ttmm) REVERT: A 654 MET cc_start: 0.8903 (tpp) cc_final: 0.8597 (tpp) REVERT: A 702 LYS cc_start: 0.8329 (tmtt) cc_final: 0.7896 (ttpp) REVERT: B 41 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 71 THR cc_start: 0.8255 (p) cc_final: 0.7928 (p) REVERT: B 134 TRP cc_start: 0.7996 (p90) cc_final: 0.7602 (p90) REVERT: B 140 MET cc_start: 0.7210 (mtp) cc_final: 0.6995 (mtm) REVERT: B 147 GLN cc_start: 0.8265 (mm110) cc_final: 0.8029 (mm110) REVERT: B 148 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8847 (mp) REVERT: B 184 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6762 (pttt) REVERT: B 222 ARG cc_start: 0.8545 (ttm170) cc_final: 0.7799 (ttt180) REVERT: B 248 MET cc_start: 0.7652 (tpp) cc_final: 0.7040 (tpp) REVERT: B 266 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 388 ASP cc_start: 0.8197 (m-30) cc_final: 0.7733 (m-30) REVERT: B 523 ASP cc_start: 0.7963 (m-30) cc_final: 0.7493 (m-30) REVERT: B 615 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: C 38 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7612 (m100) REVERT: C 44 GLU cc_start: 0.6411 (tp30) cc_final: 0.5897 (tp30) REVERT: C 74 PRO cc_start: 0.7738 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: C 164 LYS cc_start: 0.8833 (tppt) cc_final: 0.7846 (tppt) REVERT: C 168 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: C 176 GLU cc_start: 0.7921 (mp0) cc_final: 0.7577 (pm20) REVERT: C 234 GLU cc_start: 0.7801 (pm20) cc_final: 0.7206 (pp20) outliers start: 42 outliers final: 21 residues processed: 271 average time/residue: 0.2482 time to fit residues: 96.5446 Evaluate side-chains 266 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112982 restraints weight = 19429.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116489 restraints weight = 10092.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118857 restraints weight = 6594.686| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12687 Z= 0.117 Angle : 0.594 10.274 17180 Z= 0.297 Chirality : 0.041 0.161 1886 Planarity : 0.004 0.049 2080 Dihedral : 13.008 165.804 2006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 3.03 % Allowed : 17.86 % Favored : 79.11 % 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: -0.87 (0.22), residues: 1445 helix: 0.88 (0.21), residues: 666 sheet: -0.29 (0.52), residues: 122 loop : -2.27 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 PHE 0.017 0.001 PHE C 212 TYR 0.016 0.001 TYR C 11 ARG 0.012 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 515) hydrogen bonds : angle 4.07723 ( 1430) covalent geometry : bond 0.00266 (12687) covalent geometry : angle 0.59368 (17180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7073 (ttm) REVERT: A 221 ASN cc_start: 0.8530 (t0) cc_final: 0.8137 (t0) REVERT: A 222 GLN cc_start: 0.8079 (mm110) cc_final: 0.7340 (mm-40) REVERT: A 244 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 382 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: A 387 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 425 GLU cc_start: 0.8033 (tp30) cc_final: 0.7800 (mm-30) REVERT: A 426 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 427 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8699 (tt) REVERT: A 654 MET cc_start: 0.9035 (tpp) cc_final: 0.8743 (tpp) REVERT: A 702 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7749 (ttpp) REVERT: B 41 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7009 (tm-30) REVERT: B 71 THR cc_start: 0.8245 (p) cc_final: 0.7931 (p) REVERT: B 140 MET cc_start: 0.7149 (mtp) cc_final: 0.6818 (mtm) REVERT: B 148 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 184 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6786 (pttt) REVERT: B 222 ARG cc_start: 0.8492 (ttm170) cc_final: 0.7714 (ttt180) REVERT: B 248 MET cc_start: 0.7750 (tpp) cc_final: 0.7120 (tpp) REVERT: B 388 ASP cc_start: 0.8200 (m-30) cc_final: 0.7725 (m-30) REVERT: B 523 ASP cc_start: 0.8085 (m-30) cc_final: 0.7657 (m-30) REVERT: B 578 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8236 (mtp85) REVERT: C 38 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7578 (m100) REVERT: C 74 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7676 (Cg_endo) REVERT: C 164 LYS cc_start: 0.8870 (tppt) cc_final: 0.7914 (tppt) REVERT: C 168 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (mp0) outliers start: 39 outliers final: 23 residues processed: 264 average time/residue: 0.2712 time to fit residues: 104.4761 Evaluate side-chains 267 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 35 optimal weight: 0.0170 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114842 restraints weight = 19277.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118343 restraints weight = 9939.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120723 restraints weight = 6475.762| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12687 Z= 0.112 Angle : 0.606 8.640 17180 Z= 0.304 Chirality : 0.041 0.158 1886 Planarity : 0.004 0.048 2080 Dihedral : 12.981 165.198 2006 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 2.33 % Allowed : 18.48 % Favored : 79.19 % 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: -0.73 (0.22), residues: 1445 helix: 1.01 (0.21), residues: 662 sheet: -0.15 (0.52), residues: 119 loop : -2.19 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 357 HIS 0.005 0.001 HIS A 451 PHE 0.024 0.001 PHE B 108 TYR 0.012 0.001 TYR B 692 ARG 0.011 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 515) hydrogen bonds : angle 3.98322 ( 1430) covalent geometry : bond 0.00251 (12687) covalent geometry : angle 0.60620 (17180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6779 (ttm) REVERT: A 196 MET cc_start: 0.8268 (tmm) cc_final: 0.7541 (tmm) REVERT: A 221 ASN cc_start: 0.8518 (t0) cc_final: 0.8140 (t0) REVERT: A 222 GLN cc_start: 0.8105 (mm110) cc_final: 0.7376 (mm-40) REVERT: A 382 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: A 387 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8732 (mm) REVERT: A 425 GLU cc_start: 0.8014 (tp30) cc_final: 0.7776 (mm-30) REVERT: A 426 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 427 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 654 MET cc_start: 0.8946 (tpp) cc_final: 0.8665 (tpp) REVERT: A 702 LYS cc_start: 0.8203 (tmtt) cc_final: 0.7738 (ttpp) REVERT: B 41 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 71 THR cc_start: 0.8295 (p) cc_final: 0.7987 (p) REVERT: B 140 MET cc_start: 0.7132 (mtp) cc_final: 0.6777 (mtm) REVERT: B 148 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8765 (mp) REVERT: B 222 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7342 (ttt180) REVERT: B 248 MET cc_start: 0.7819 (tpp) cc_final: 0.7225 (tpp) REVERT: B 388 ASP cc_start: 0.8203 (m-30) cc_final: 0.7719 (m-30) REVERT: B 523 ASP cc_start: 0.8050 (m-30) cc_final: 0.7629 (m-30) REVERT: B 578 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8220 (mtp85) REVERT: B 710 MET cc_start: 0.8167 (mmm) cc_final: 0.7813 (tpt) REVERT: B 740 LYS cc_start: 0.7950 (pttt) cc_final: 0.7746 (pttt) REVERT: C 38 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7619 (m100) REVERT: C 51 MET cc_start: 0.8218 (tpp) cc_final: 0.8004 (tpp) REVERT: C 176 GLU cc_start: 0.7983 (mp0) cc_final: 0.7641 (pm20) REVERT: C 234 GLU cc_start: 0.7946 (pm20) cc_final: 0.7120 (pp20) outliers start: 30 outliers final: 20 residues processed: 258 average time/residue: 0.2471 time to fit residues: 91.9555 Evaluate side-chains 254 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 130 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106314 restraints weight = 19450.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109780 restraints weight = 10286.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112096 restraints weight = 6852.442| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12687 Z= 0.188 Angle : 0.682 10.120 17180 Z= 0.342 Chirality : 0.044 0.202 1886 Planarity : 0.004 0.061 2080 Dihedral : 13.145 166.211 2006 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 2.41 % Allowed : 18.63 % Favored : 78.96 % 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: -0.81 (0.22), residues: 1445 helix: 0.91 (0.20), residues: 661 sheet: -0.26 (0.54), residues: 115 loop : -2.17 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 357 HIS 0.006 0.001 HIS A 451 PHE 0.024 0.002 PHE B 108 TYR 0.016 0.001 TYR C 11 ARG 0.010 0.001 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 515) hydrogen bonds : angle 4.18975 ( 1430) covalent geometry : bond 0.00438 (12687) covalent geometry : angle 0.68166 (17180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6802 (ttm) REVERT: A 196 MET cc_start: 0.8266 (tmm) cc_final: 0.7559 (tmm) REVERT: A 387 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8770 (mm) REVERT: A 426 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 427 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 654 MET cc_start: 0.9033 (tpp) cc_final: 0.8778 (tpp) REVERT: B 41 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 71 THR cc_start: 0.8415 (p) cc_final: 0.8113 (p) REVERT: B 140 MET cc_start: 0.7501 (mtp) cc_final: 0.7182 (mtt) REVERT: B 222 ARG cc_start: 0.8438 (ttm170) cc_final: 0.7513 (ttt180) REVERT: B 248 MET cc_start: 0.8075 (tpp) cc_final: 0.7608 (tpp) REVERT: B 353 MET cc_start: 0.7858 (mmp) cc_final: 0.7631 (mmp) REVERT: B 388 ASP cc_start: 0.8204 (m-30) cc_final: 0.7951 (m-30) REVERT: B 523 ASP cc_start: 0.8035 (m-30) cc_final: 0.7551 (m-30) REVERT: B 578 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8201 (mtp85) REVERT: B 710 MET cc_start: 0.8228 (mmm) cc_final: 0.7895 (tpt) REVERT: C 38 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7653 (m100) REVERT: C 44 GLU cc_start: 0.6604 (tp30) cc_final: 0.6285 (pm20) REVERT: C 234 GLU cc_start: 0.7992 (pm20) cc_final: 0.7283 (pp20) outliers start: 31 outliers final: 21 residues processed: 243 average time/residue: 0.2397 time to fit residues: 84.0836 Evaluate side-chains 245 residues out of total 1301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 285 GLN A 456 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113089 restraints weight = 19339.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116601 restraints weight = 10031.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118925 restraints weight = 6520.288| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12687 Z= 0.117 Angle : 0.644 11.480 17180 Z= 0.322 Chirality : 0.042 0.166 1886 Planarity : 0.004 0.051 2080 Dihedral : 13.028 165.411 2006 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 2.02 % Allowed : 19.25 % Favored : 78.73 % 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: -0.76 (0.22), residues: 1445 helix: 0.94 (0.21), residues: 662 sheet: -0.12 (0.54), residues: 111 loop : -2.14 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.024 0.001 PHE B 108 TYR 0.010 0.001 TYR B 692 ARG 0.010 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 515) hydrogen bonds : angle 4.09350 ( 1430) covalent geometry : bond 0.00265 (12687) covalent geometry : angle 0.64428 (17180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.90 seconds wall clock time: 82 minutes 37.65 seconds (4957.65 seconds total)