Starting phenix.real_space_refine on Thu Jul 2 02:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.map" model { file = "/net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnj_34166/07_2026/8gnj_34166.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 1 5.49 5 S 28 5.16 5 C 3670 2.51 5 N 1042 2.21 5 O 1091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3821 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.16, per 1000 atoms: 0.20 Number of scatterers: 5832 At special positions: 0 Unit cell: (92.536, 93.612, 117.284, 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 28 16.00 P 1 15.00 O 1091 8.00 N 1042 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.45 Conformation dependent library (CDL) restraints added in 247.1 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 3 sheets defined 59.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.846A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.498A pdb=" N SER A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 92 through 104 removed outlier: 3.961A pdb=" N PHE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.673A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 125 through 132 removed outlier: 4.398A pdb=" N LEU A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 4.029A pdb=" N ARG A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.115A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.544A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.922A pdb=" N ARG A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.586A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.738A pdb=" N ARG A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.686A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.773A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.855A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.606A pdb=" N ALA A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 removed outlier: 4.059A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 370 through 379 removed outlier: 4.526A pdb=" N SER A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.511A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 475 removed outlier: 4.052A pdb=" N GLU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.818A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.568A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 509 removed outlier: 4.010A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.695A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 518' Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.536A pdb=" N ASP A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 3.757A pdb=" N GLU A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.642A pdb=" N ALA B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.770A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.649A pdb=" N LYS C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.737A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE B 617 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 681 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.667A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.498A pdb=" N GLY C 11 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET C 35 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP C 37 " --> pdb=" O VAL C 49 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1662 1.33 - 1.45: 1102 1.45 - 1.58: 3127 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 5930 Sorted by residual: bond pdb=" O5R NMN A1001 " pdb=" P NMN A1001 " ideal model delta sigma weight residual 1.730 1.610 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C SER A 319 " pdb=" O SER A 319 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.16e-02 7.43e+03 1.65e+01 bond pdb=" C5R NMN A1001 " pdb=" O5R NMN A1001 " ideal model delta sigma weight residual 1.389 1.448 -0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" CA SER A 319 " pdb=" CB SER A 319 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.57e-02 4.06e+03 8.52e+00 bond pdb=" C GLY A 89 " pdb=" O GLY A 89 " ideal model delta sigma weight residual 1.236 1.272 -0.036 1.35e-02 5.49e+03 7.10e+00 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 7663 2.87 - 5.73: 308 5.73 - 8.60: 40 8.60 - 11.47: 11 11.47 - 14.33: 4 Bond angle restraints: 8026 Sorted by residual: angle pdb=" N LYS A 80 " pdb=" CA LYS A 80 " pdb=" C LYS A 80 " ideal model delta sigma weight residual 113.20 105.31 7.89 1.21e+00 6.83e-01 4.25e+01 angle pdb=" N PRO A 549 " pdb=" CA PRO A 549 " pdb=" CB PRO A 549 " ideal model delta sigma weight residual 103.00 97.73 5.27 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C GLU A 284 " pdb=" N ARG A 285 " pdb=" CA ARG A 285 " ideal model delta sigma weight residual 121.58 112.70 8.88 1.95e+00 2.63e-01 2.07e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 112.23 106.58 5.65 1.26e+00 6.30e-01 2.01e+01 angle pdb=" N HIS A 547 " pdb=" CA HIS A 547 " pdb=" C HIS A 547 " ideal model delta sigma weight residual 111.54 105.63 5.91 1.36e+00 5.41e-01 1.89e+01 ... (remaining 8021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3230 17.51 - 35.02: 290 35.02 - 52.53: 66 52.53 - 70.04: 29 70.04 - 87.55: 8 Dihedral angle restraints: 3623 sinusoidal: 1480 harmonic: 2143 Sorted by residual: dihedral pdb=" CA VAL A 95 " pdb=" C VAL A 95 " pdb=" N PHE A 96 " pdb=" CA PHE A 96 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " pdb=" CA ALA A 85 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LYS C 76 " pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 736 0.085 - 0.170: 153 0.170 - 0.256: 24 0.256 - 0.341: 2 0.341 - 0.426: 1 Chirality restraints: 916 Sorted by residual: chirality pdb=" CG LEU A 148 " pdb=" CB LEU A 148 " pdb=" CD1 LEU A 148 " pdb=" CD2 LEU A 148 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA LYS A 80 " pdb=" N LYS A 80 " pdb=" C LYS A 80 " pdb=" CB LYS A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 913 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 99 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C VAL A 99 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL A 99 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 545 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C MET A 545 " 0.069 2.00e-02 2.50e+03 pdb=" O MET A 545 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 546 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 63 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASP A 63 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 63 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 34 2.43 - 3.05: 3602 3.05 - 3.66: 8979 3.66 - 4.28: 12574 4.28 - 4.90: 20605 Nonbonded interactions: 45794 Sorted by model distance: nonbonded pdb=" NH1 ARG A 216 " pdb=" NE2 GLN B 688 " model vdw 1.811 3.200 nonbonded pdb=" OE2 GLU A 400 " pdb=" O VAL A 401 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU A 76 " pdb=" NZ LYS A 80 " model vdw 2.184 3.540 nonbonded pdb=" OG1 THR A 447 " pdb=" OE1 GLU A 450 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP A 441 " pdb=" OH TYR A 503 " model vdw 2.258 3.040 ... (remaining 45789 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: 2.540 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.011 0.120 5931 Z= 0.516 Angle : 1.341 14.332 8028 Z= 0.719 Chirality : 0.072 0.426 916 Planarity : 0.008 0.059 1040 Dihedral : 15.796 87.554 2236 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.26), residues: 740 helix: -3.26 (0.18), residues: 384 sheet: -0.37 (0.71), residues: 56 loop : -1.50 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.002 ARG A 182 TYR 0.011 0.003 TYR A 213 PHE 0.022 0.003 PHE A 96 TRP 0.019 0.003 TRP B 638 HIS 0.019 0.003 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.52 ( 5930) covalent geometry : angle 1.34114 / 0.72 ( 8026) SS BOND : bond 0.00739 / 0.46 ( 1) SS BOND : angle 1.35176 / 0.54 ( 2) hydrogen bonds : bond 0.18595 / 12.47 ( 246) hydrogen bonds : angle 7.42113 / 5.15 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.9160 (t80) cc_final: 0.8843 (t80) REVERT: A 284 GLU cc_start: 0.6353 (pt0) cc_final: 0.5927 (pt0) REVERT: A 312 LEU cc_start: 0.9201 (mt) cc_final: 0.8943 (mt) REVERT: A 326 ASP cc_start: 0.8951 (t0) cc_final: 0.8740 (t0) REVERT: A 335 ASP cc_start: 0.8176 (p0) cc_final: 0.7931 (p0) REVERT: A 391 LYS cc_start: 0.9065 (mttp) cc_final: 0.8590 (mttp) REVERT: B 581 LYS cc_start: 0.8836 (tptt) cc_final: 0.8428 (tptt) REVERT: B 606 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6610 (ttpt) REVERT: B 617 PHE cc_start: 0.8252 (t80) cc_final: 0.7985 (t80) REVERT: C 14 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7692 (mm-40) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1158 time to fit residues: 33.1854 Evaluate side-chains 178 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 232 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113027 restraints weight = 11748.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111269 restraints weight = 8113.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111865 restraints weight = 9627.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112508 restraints weight = 6170.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112498 restraints weight = 5827.522| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5931 Z= 0.197 Angle : 0.758 10.856 8028 Z= 0.379 Chirality : 0.045 0.203 916 Planarity : 0.005 0.048 1040 Dihedral : 7.098 55.422 844 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.38 % Allowed : 14.98 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.30), residues: 740 helix: -1.63 (0.24), residues: 383 sheet: -0.19 (0.69), residues: 57 loop : -0.94 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 517 TYR 0.011 0.002 TYR B 687 PHE 0.024 0.003 PHE B 565 TRP 0.012 0.002 TRP A 103 HIS 0.013 0.002 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 5930) covalent geometry : angle 0.75841 / 0.38 ( 8026) SS BOND : bond 0.00263 / 0.16 ( 1) SS BOND : angle 0.70144 / 0.33 ( 2) hydrogen bonds : bond 0.04473 / 3.00 ( 246) hydrogen bonds : angle 5.01726 / 3.48 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8001 (t-100) cc_final: 0.7725 (t-100) REVERT: A 156 ASN cc_start: 0.9087 (m-40) cc_final: 0.8804 (m-40) REVERT: A 189 GLU cc_start: 0.8061 (tt0) cc_final: 0.7857 (tt0) REVERT: A 214 TRP cc_start: 0.7982 (m-10) cc_final: 0.7770 (m-10) REVERT: A 335 ASP cc_start: 0.7936 (p0) cc_final: 0.7640 (p0) REVERT: B 581 LYS cc_start: 0.8699 (tptt) cc_final: 0.8339 (tptt) REVERT: B 617 PHE cc_start: 0.7970 (t80) cc_final: 0.7711 (t80) outliers start: 21 outliers final: 16 residues processed: 194 average time/residue: 0.0957 time to fit residues: 23.0653 Evaluate side-chains 182 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112142 restraints weight = 11512.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110817 restraints weight = 7494.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111724 restraints weight = 7712.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111769 restraints weight = 5319.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111998 restraints weight = 5729.454| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5931 Z= 0.176 Angle : 0.709 10.332 8028 Z= 0.348 Chirality : 0.044 0.179 916 Planarity : 0.005 0.042 1040 Dihedral : 6.736 57.833 844 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.35 % Allowed : 17.07 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.30), residues: 740 helix: -0.93 (0.26), residues: 381 sheet: 0.26 (0.69), residues: 57 loop : -0.75 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 53 TYR 0.009 0.001 TYR C 54 PHE 0.021 0.002 PHE A 192 TRP 0.011 0.001 TRP B 638 HIS 0.010 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 5930) covalent geometry : angle 0.70911 / 0.35 ( 8026) SS BOND : bond 0.00311 / 0.19 ( 1) SS BOND : angle 0.51588 / 0.24 ( 2) hydrogen bonds : bond 0.03859 / 2.58 ( 246) hydrogen bonds : angle 4.50118 / 3.14 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8151 (t) cc_final: 0.7942 (t) REVERT: A 114 GLN cc_start: 0.8659 (pm20) cc_final: 0.8288 (pm20) REVERT: A 156 ASN cc_start: 0.9075 (m-40) cc_final: 0.8817 (m-40) REVERT: A 214 TRP cc_start: 0.7926 (m-10) cc_final: 0.7676 (m-10) REVERT: A 335 ASP cc_start: 0.7783 (p0) cc_final: 0.7543 (p0) REVERT: A 514 LEU cc_start: 0.8810 (tp) cc_final: 0.8467 (tt) REVERT: B 581 LYS cc_start: 0.8669 (tptt) cc_final: 0.8399 (tptt) REVERT: B 606 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6844 (ttpp) REVERT: B 612 MET cc_start: 0.8133 (mmp) cc_final: 0.7775 (mtm) REVERT: B 617 PHE cc_start: 0.8005 (t80) cc_final: 0.7706 (t80) REVERT: B 637 ASP cc_start: 0.6548 (p0) cc_final: 0.6054 (t0) outliers start: 27 outliers final: 20 residues processed: 199 average time/residue: 0.0918 time to fit residues: 23.0035 Evaluate side-chains 186 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114434 restraints weight = 11702.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112153 restraints weight = 9835.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113058 restraints weight = 10831.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113308 restraints weight = 6933.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113546 restraints weight = 7008.771| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5931 Z= 0.163 Angle : 0.692 10.046 8028 Z= 0.337 Chirality : 0.044 0.187 916 Planarity : 0.004 0.044 1040 Dihedral : 6.400 58.968 844 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 20.13 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.31), residues: 740 helix: -0.70 (0.26), residues: 389 sheet: 0.52 (0.69), residues: 57 loop : -0.64 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 53 TYR 0.009 0.001 TYR C 54 PHE 0.022 0.002 PHE B 565 TRP 0.023 0.001 TRP A 103 HIS 0.013 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 5930) covalent geometry : angle 0.69198 / 0.34 ( 8026) SS BOND : bond 0.00297 / 0.19 ( 1) SS BOND : angle 0.46784 / 0.22 ( 2) hydrogen bonds : bond 0.03536 / 2.35 ( 246) hydrogen bonds : angle 4.34229 / 3.05 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8529 (pm20) cc_final: 0.8180 (pm20) REVERT: A 156 ASN cc_start: 0.8974 (m-40) cc_final: 0.8716 (m-40) REVERT: A 191 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8450 (mmm) REVERT: A 193 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8368 (mtpt) REVERT: A 214 TRP cc_start: 0.7825 (m-10) cc_final: 0.7598 (m-10) REVERT: A 335 ASP cc_start: 0.7709 (p0) cc_final: 0.7485 (p0) REVERT: A 514 LEU cc_start: 0.8884 (tp) cc_final: 0.8565 (tt) REVERT: B 581 LYS cc_start: 0.8694 (tptt) cc_final: 0.8390 (tptt) REVERT: B 612 MET cc_start: 0.8070 (mmp) cc_final: 0.7774 (mtm) REVERT: B 617 PHE cc_start: 0.7920 (t80) cc_final: 0.7694 (t80) REVERT: B 637 ASP cc_start: 0.6647 (p0) cc_final: 0.6233 (t0) outliers start: 23 outliers final: 17 residues processed: 189 average time/residue: 0.0755 time to fit residues: 17.9290 Evaluate side-chains 181 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116009 restraints weight = 11783.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113778 restraints weight = 10080.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114688 restraints weight = 10985.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115092 restraints weight = 6641.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115340 restraints weight = 6474.412| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5931 Z= 0.134 Angle : 0.669 9.017 8028 Z= 0.326 Chirality : 0.042 0.198 916 Planarity : 0.004 0.043 1040 Dihedral : 6.098 53.951 844 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 21.58 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.31), residues: 740 helix: -0.54 (0.27), residues: 398 sheet: 0.61 (0.71), residues: 57 loop : -0.60 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 53 TYR 0.007 0.001 TYR C 54 PHE 0.020 0.002 PHE B 565 TRP 0.018 0.001 TRP B 638 HIS 0.014 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 5930) covalent geometry : angle 0.66871 / 0.33 ( 8026) SS BOND : bond 0.00234 / 0.15 ( 1) SS BOND : angle 0.45966 / 0.21 ( 2) hydrogen bonds : bond 0.03087 / 2.06 ( 246) hydrogen bonds : angle 4.18930 / 2.94 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.9019 (t0) cc_final: 0.8351 (m-40) REVERT: A 214 TRP cc_start: 0.7780 (m-10) cc_final: 0.7550 (m-10) REVERT: A 335 ASP cc_start: 0.7813 (p0) cc_final: 0.7551 (p0) REVERT: A 348 TYR cc_start: 0.7624 (t80) cc_final: 0.7300 (t80) REVERT: A 473 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 581 LYS cc_start: 0.8674 (tptt) cc_final: 0.8423 (tptt) REVERT: B 606 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6533 (ttpt) REVERT: B 617 PHE cc_start: 0.7963 (t80) cc_final: 0.7743 (t80) REVERT: B 637 ASP cc_start: 0.6531 (p0) cc_final: 0.6327 (t0) REVERT: C 95 TYR cc_start: 0.8846 (m-80) cc_final: 0.8628 (m-80) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.0769 time to fit residues: 18.0505 Evaluate side-chains 183 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 232 ASN ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111867 restraints weight = 11673.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110076 restraints weight = 12076.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110893 restraints weight = 12006.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112540 restraints weight = 7149.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112638 restraints weight = 5935.039| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5931 Z= 0.246 Angle : 0.745 11.687 8028 Z= 0.370 Chirality : 0.046 0.267 916 Planarity : 0.005 0.046 1040 Dihedral : 6.237 47.191 844 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.15 % Allowed : 22.06 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.31), residues: 740 helix: -0.70 (0.26), residues: 404 sheet: 0.72 (0.71), residues: 57 loop : -0.70 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 216 TYR 0.009 0.001 TYR A 213 PHE 0.021 0.002 PHE B 565 TRP 0.018 0.001 TRP A 103 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 5930) covalent geometry : angle 0.74471 / 0.37 ( 8026) SS BOND : bond 0.00470 / 0.29 ( 1) SS BOND : angle 0.37403 / 0.18 ( 2) hydrogen bonds : bond 0.03869 / 2.56 ( 246) hydrogen bonds : angle 4.51272 / 3.15 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8510 (pm20) cc_final: 0.8182 (pm20) REVERT: A 156 ASN cc_start: 0.8912 (t0) cc_final: 0.8601 (m-40) REVERT: A 180 LEU cc_start: 0.8621 (tp) cc_final: 0.8404 (tt) REVERT: A 193 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8377 (mtpt) REVERT: A 214 TRP cc_start: 0.7854 (m-10) cc_final: 0.7637 (m-10) REVERT: A 255 PHE cc_start: 0.8917 (t80) cc_final: 0.8681 (t80) REVERT: B 581 LYS cc_start: 0.8745 (tptt) cc_final: 0.8471 (tptt) REVERT: B 637 ASP cc_start: 0.6593 (p0) cc_final: 0.6345 (t0) outliers start: 32 outliers final: 24 residues processed: 187 average time/residue: 0.0795 time to fit residues: 18.7065 Evaluate side-chains 185 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113948 restraints weight = 11542.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113090 restraints weight = 9544.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114231 restraints weight = 7640.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114518 restraints weight = 5272.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115096 restraints weight = 5015.718| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5931 Z= 0.156 Angle : 0.718 9.618 8028 Z= 0.350 Chirality : 0.044 0.226 916 Planarity : 0.004 0.046 1040 Dihedral : 6.292 54.704 844 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.86 % Allowed : 24.96 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.31), residues: 740 helix: -0.54 (0.26), residues: 397 sheet: 0.73 (0.71), residues: 57 loop : -0.59 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 53 TYR 0.007 0.001 TYR C 95 PHE 0.015 0.002 PHE A 96 TRP 0.043 0.002 TRP A 103 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 5930) covalent geometry : angle 0.71805 / 0.35 ( 8026) SS BOND : bond 0.00271 / 0.17 ( 1) SS BOND : angle 0.50614 / 0.23 ( 2) hydrogen bonds : bond 0.03241 / 2.17 ( 246) hydrogen bonds : angle 4.30469 / 3.02 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.9023 (t0) cc_final: 0.8668 (m-40) REVERT: A 214 TRP cc_start: 0.7840 (m-10) cc_final: 0.7624 (m-10) REVERT: B 581 LYS cc_start: 0.8770 (tptt) cc_final: 0.8500 (tptt) REVERT: C 95 TYR cc_start: 0.8902 (m-80) cc_final: 0.8690 (m-80) outliers start: 24 outliers final: 21 residues processed: 188 average time/residue: 0.0724 time to fit residues: 17.3946 Evaluate side-chains 184 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117567 restraints weight = 11544.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115446 restraints weight = 10890.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116705 restraints weight = 9404.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117043 restraints weight = 6368.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117613 restraints weight = 6178.274| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5931 Z= 0.137 Angle : 0.716 9.284 8028 Z= 0.350 Chirality : 0.043 0.210 916 Planarity : 0.004 0.055 1040 Dihedral : 6.292 59.904 844 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.90 % Allowed : 25.12 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.31), residues: 740 helix: -0.42 (0.27), residues: 395 sheet: 0.36 (0.67), residues: 63 loop : -0.54 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 53 TYR 0.008 0.001 TYR C 95 PHE 0.014 0.002 PHE A 96 TRP 0.035 0.001 TRP A 103 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5930) covalent geometry : angle 0.71589 / 0.35 ( 8026) SS BOND : bond 0.00212 / 0.13 ( 1) SS BOND : angle 0.46943 / 0.22 ( 2) hydrogen bonds : bond 0.03071 / 2.10 ( 246) hydrogen bonds : angle 4.23695 / 2.97 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8909 (t0) cc_final: 0.8611 (m-40) REVERT: A 391 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8791 (mtmm) REVERT: B 569 ARG cc_start: 0.6627 (tpp-160) cc_final: 0.6168 (tpp-160) REVERT: B 581 LYS cc_start: 0.8754 (tptt) cc_final: 0.8497 (tptt) REVERT: B 637 ASP cc_start: 0.5343 (t0) cc_final: 0.4375 (p0) outliers start: 18 outliers final: 16 residues processed: 178 average time/residue: 0.0936 time to fit residues: 20.8803 Evaluate side-chains 177 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116402 restraints weight = 11504.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114490 restraints weight = 9254.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115552 restraints weight = 8601.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115812 restraints weight = 5985.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116133 restraints weight = 5896.614| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5931 Z= 0.144 Angle : 0.736 9.351 8028 Z= 0.358 Chirality : 0.043 0.198 916 Planarity : 0.004 0.043 1040 Dihedral : 6.039 53.866 844 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.22 % Allowed : 25.76 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.31), residues: 740 helix: -0.43 (0.26), residues: 401 sheet: 0.30 (0.66), residues: 63 loop : -0.58 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 216 TYR 0.008 0.001 TYR C 54 PHE 0.023 0.002 PHE A 255 TRP 0.032 0.002 TRP A 103 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 5930) covalent geometry : angle 0.73600 / 0.36 ( 8026) SS BOND : bond 0.00233 / 0.15 ( 1) SS BOND : angle 0.52233 / 0.24 ( 2) hydrogen bonds : bond 0.03169 / 2.17 ( 246) hydrogen bonds : angle 4.25694 / 3.00 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8915 (t0) cc_final: 0.8584 (m-40) REVERT: B 569 ARG cc_start: 0.6654 (tpp-160) cc_final: 0.6180 (tpp-160) REVERT: B 581 LYS cc_start: 0.8732 (tptt) cc_final: 0.8493 (tptt) REVERT: B 637 ASP cc_start: 0.5756 (t0) cc_final: 0.4723 (p0) outliers start: 20 outliers final: 20 residues processed: 176 average time/residue: 0.0855 time to fit residues: 18.9827 Evaluate side-chains 180 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115486 restraints weight = 11564.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113804 restraints weight = 9446.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114665 restraints weight = 9257.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115048 restraints weight = 6245.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115581 restraints weight = 5557.915| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5931 Z= 0.156 Angle : 0.756 10.283 8028 Z= 0.367 Chirality : 0.044 0.207 916 Planarity : 0.005 0.056 1040 Dihedral : 6.011 51.982 844 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.70 % Allowed : 25.76 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.31), residues: 740 helix: -0.42 (0.26), residues: 401 sheet: 0.28 (0.66), residues: 63 loop : -0.56 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 53 TYR 0.007 0.001 TYR A 348 PHE 0.017 0.002 PHE A 96 TRP 0.031 0.002 TRP A 103 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 5930) covalent geometry : angle 0.75592 / 0.37 ( 8026) SS BOND : bond 0.00290 / 0.18 ( 1) SS BOND : angle 0.54465 / 0.25 ( 2) hydrogen bonds : bond 0.03261 / 2.22 ( 246) hydrogen bonds : angle 4.36541 / 3.07 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8910 (t0) cc_final: 0.8583 (m-40) REVERT: A 449 GLU cc_start: 0.7321 (pm20) cc_final: 0.7118 (pm20) REVERT: B 569 ARG cc_start: 0.6711 (tpp-160) cc_final: 0.6220 (tpp-160) REVERT: B 581 LYS cc_start: 0.8718 (tptt) cc_final: 0.8488 (tptt) REVERT: B 637 ASP cc_start: 0.5832 (t0) cc_final: 0.4665 (p0) outliers start: 23 outliers final: 21 residues processed: 172 average time/residue: 0.0826 time to fit residues: 18.1775 Evaluate side-chains 177 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 0.0010 chunk 71 optimal weight: 0.0070 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117109 restraints weight = 11487.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114910 restraints weight = 9604.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115679 restraints weight = 10535.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116216 restraints weight = 6999.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116534 restraints weight = 6219.733| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5931 Z= 0.145 Angle : 0.755 11.325 8028 Z= 0.367 Chirality : 0.043 0.202 916 Planarity : 0.004 0.042 1040 Dihedral : 5.891 50.455 844 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.54 % Allowed : 26.09 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.31), residues: 740 helix: -0.39 (0.26), residues: 401 sheet: 0.31 (0.66), residues: 63 loop : -0.47 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 216 TYR 0.009 0.001 TYR C 54 PHE 0.030 0.002 PHE A 255 TRP 0.039 0.002 TRP A 214 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 ( 5930) covalent geometry : angle 0.75535 / 0.37 ( 8026) SS BOND : bond 0.00254 / 0.16 ( 1) SS BOND : angle 0.55041 / 0.26 ( 2) hydrogen bonds : bond 0.03223 / 2.23 ( 246) hydrogen bonds : angle 4.34467 / 3.05 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.07 seconds wall clock time: 20 minutes 25.96 seconds (1225.96 seconds total)