Starting phenix.real_space_refine on Wed Feb 4 06:39:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.map" model { file = "/net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hiv_52202/02_2026/9hiv_52202.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5762 2.51 5 N 1502 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4201 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 3 Chain: "D" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1622 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain: "F" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3181 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 12, 'TRANS': 393} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 9004 At special positions: 0 Unit cell: (104.34, 121.36, 116.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1706 8.00 N 1502 7.00 C 5762 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: 0.58 Conformation dependent library (CDL) restraints added in 334.4 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 24.8% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.212A pdb=" N ARG A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.936A pdb=" N VAL A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.724A pdb=" N GLY A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 526 through 530 removed outlier: 4.252A pdb=" N LYS A 530 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 82 through 97 removed outlier: 3.976A pdb=" N TYR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.725A pdb=" N ALA D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 142 removed outlier: 3.748A pdb=" N TYR D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 177 removed outlier: 4.361A pdb=" N GLU D 150 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 Processing helix chain 'D' and resid 203 through 222 removed outlier: 3.604A pdb=" N TYR D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.671A pdb=" N ALA D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 33 Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.554A pdb=" N ALA F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 removed outlier: 3.535A pdb=" N TYR F 70 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR F 71 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 72 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 73 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 226 removed outlier: 4.336A pdb=" N LYS F 226 " --> pdb=" O ALA F 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 226' Processing helix chain 'F' and resid 300 through 303 Processing helix chain 'F' and resid 311 through 322 Processing helix chain 'F' and resid 344 through 348 Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.723A pdb=" N ASP A 322 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU A 296 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU A 368 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN A 298 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N MET A 370 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 300 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 372 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 302 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLU A 374 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 361 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 353 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 386 removed outlier: 4.300A pdb=" N ILE A 380 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE A 446 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS A 382 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 448 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN A 384 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475 removed outlier: 4.293A pdb=" N SER A 591 " --> pdb=" O LYS A 626 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 626 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 795 " --> pdb=" O TRP A 826 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP A 826 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG A 797 " --> pdb=" O ASN A 824 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASN A 824 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY A 799 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA A 822 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU A 801 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 820 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG A 803 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY A 818 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 816 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 807 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 757 through 759 removed outlier: 6.277A pdb=" N ASP A 758 " --> pdb=" O ILE A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 38 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 37 through 38 current: chain 'F' and resid 96 through 115 removed outlier: 13.180A pdb=" N SER F 104 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 13.962A pdb=" N SER F 128 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASP F 106 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 118 through 129 current: chain 'F' and resid 145 through 168 removed outlier: 3.734A pdb=" N SER F 149 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR F 201 " --> pdb=" O MET F 190 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 228 through 237 current: chain 'F' and resid 261 through 262 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 261 through 262 current: chain 'F' and resid 289 through 298 removed outlier: 3.663A pdb=" N THR F 328 " --> pdb=" O THR F 359 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 370 through 379 current: chain 'F' and resid 408 through 423 Processing sheet with id=AA6, first strand: chain 'F' and resid 240 through 242 removed outlier: 4.604A pdb=" N PHE F 271 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP F 268 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL F 308 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 306 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 363 through 364 removed outlier: 3.572A pdb=" N LYS F 367 " --> pdb=" O ILE F 364 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1089 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: 1.41 Time building geometry restraints manager: 0.80 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: 1500 1.32 - 1.45: 2687 1.45 - 1.57: 4975 1.57 - 1.69: 1 1.69 - 1.82: 64 Bond restraints: 9227 Sorted by residual: bond pdb=" CB MET A 700 " pdb=" CG MET A 700 " ideal model delta sigma weight residual 1.520 1.403 0.117 3.00e-02 1.11e+03 1.51e+01 bond pdb=" CE LYS A 593 " pdb=" NZ LYS A 593 " ideal model delta sigma weight residual 1.489 1.387 0.102 3.00e-02 1.11e+03 1.16e+01 bond pdb=" CG ARG A 659 " pdb=" CD ARG A 659 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.08e+01 bond pdb=" CG MET A 700 " pdb=" SD MET A 700 " ideal model delta sigma weight residual 1.803 1.728 0.075 2.50e-02 1.60e+03 9.01e+00 bond pdb=" CB VAL A 543 " pdb=" CG1 VAL A 543 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.70e+00 ... (remaining 9222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 12395 4.07 - 8.14: 70 8.14 - 12.22: 6 12.22 - 16.29: 1 16.29 - 20.36: 2 Bond angle restraints: 12474 Sorted by residual: angle pdb=" CG MET A 700 " pdb=" SD MET A 700 " pdb=" CE MET A 700 " ideal model delta sigma weight residual 100.90 82.20 18.70 2.20e+00 2.07e-01 7.23e+01 angle pdb=" CD LYS A 476 " pdb=" CE LYS A 476 " pdb=" NZ LYS A 476 " ideal model delta sigma weight residual 111.90 132.26 -20.36 3.20e+00 9.77e-02 4.05e+01 angle pdb=" N THR F 133 " pdb=" CA THR F 133 " pdb=" C THR F 133 " ideal model delta sigma weight residual 108.76 100.62 8.14 1.69e+00 3.50e-01 2.32e+01 angle pdb=" CA LYS A 476 " pdb=" CB LYS A 476 " pdb=" CG LYS A 476 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 angle pdb=" CB MET A 318 " pdb=" CG MET A 318 " pdb=" SD MET A 318 " ideal model delta sigma weight residual 112.70 99.18 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 12469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 4970 18.05 - 36.10: 395 36.10 - 54.15: 46 54.15 - 72.20: 15 72.20 - 90.24: 3 Dihedral angle restraints: 5429 sinusoidal: 2185 harmonic: 3244 Sorted by residual: dihedral pdb=" CD ARG F 188 " pdb=" NE ARG F 188 " pdb=" CZ ARG F 188 " pdb=" NH1 ARG F 188 " ideal model delta sinusoidal sigma weight residual 0.00 -56.75 56.75 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA ASP A 364 " pdb=" C ASP A 364 " pdb=" N SER A 365 " pdb=" CA SER A 365 " ideal model delta harmonic sigma weight residual 180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE F 364 " pdb=" C ILE F 364 " pdb=" N ASP F 365 " pdb=" CA ASP F 365 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1066 0.070 - 0.139: 204 0.139 - 0.209: 26 0.209 - 0.279: 2 0.279 - 0.349: 2 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA TRP A 607 " pdb=" N TRP A 607 " pdb=" C TRP A 607 " pdb=" CB TRP A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE F 337 " pdb=" CA ILE F 337 " pdb=" CG1 ILE F 337 " pdb=" CG2 ILE F 337 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A 641 " pdb=" CB LEU A 641 " pdb=" CD1 LEU A 641 " pdb=" CD2 LEU A 641 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1297 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 188 " 0.881 9.50e-02 1.11e+02 3.95e-01 9.48e+01 pdb=" NE ARG F 188 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG F 188 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 188 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 188 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 607 " -0.035 2.00e-02 2.50e+03 4.12e-02 4.23e+01 pdb=" CG TRP A 607 " 0.108 2.00e-02 2.50e+03 pdb=" CD1 TRP A 607 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 607 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 607 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 607 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 607 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 607 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 607 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 607 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 725 " -0.001 2.00e-02 2.50e+03 3.65e-02 2.66e+01 pdb=" CG TYR A 725 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 725 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 725 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 725 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR A 725 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 725 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 725 " -0.012 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 120 2.66 - 3.22: 8353 3.22 - 3.78: 13096 3.78 - 4.34: 18474 4.34 - 4.90: 31140 Nonbonded interactions: 71183 Sorted by model distance: nonbonded pdb=" O GLY F 36 " pdb=" OH TYR F 361 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR F 231 " pdb=" OG1 THR F 282 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP A 724 " pdb=" O TYR A 725 " model vdw 2.226 3.040 nonbonded pdb=" N GLU D 253 " pdb=" OE1 GLU D 253 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP F 211 " pdb=" N TYR F 212 " model vdw 2.267 3.120 ... (remaining 71178 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 individual isotropic 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: 6.870 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.090 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.005 0.117 9227 Z= 0.241 Angle : 0.953 20.362 12474 Z= 0.493 Chirality : 0.057 0.349 1300 Planarity : 0.013 0.395 1611 Dihedral : 13.014 90.244 3383 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.31 (0.24), residues: 1107 helix: -0.66 (0.32), residues: 234 sheet: -0.01 (0.25), residues: 421 loop : -1.75 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.002 ARG A 659 TYR 0.073 0.002 TYR A 725 PHE 0.035 0.003 PHE D 94 TRP 0.108 0.005 TRP A 607 HIS 0.007 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9227) covalent geometry : angle 0.95307 (12474) hydrogen bonds : bond 0.17961 ( 390) hydrogen bonds : angle 7.76129 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8164 (ttp) cc_final: 0.7827 (ttp) REVERT: A 592 ILE cc_start: 0.7198 (tt) cc_final: 0.6505 (tt) REVERT: F 285 TYR cc_start: 0.7841 (t80) cc_final: 0.7629 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0908 time to fit residues: 17.4845 Evaluate side-chains 96 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 502 GLN A 544 GLN A 624 ASN A 635 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN D 193 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.109932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071878 restraints weight = 20515.623| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.78 r_work: 0.3036 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9227 Z= 0.302 Angle : 0.797 15.099 12474 Z= 0.414 Chirality : 0.051 0.199 1300 Planarity : 0.005 0.050 1611 Dihedral : 5.939 23.568 1251 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.76 % Allowed : 6.41 % Favored : 91.83 % 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: -0.98 (0.25), residues: 1107 helix: 0.03 (0.32), residues: 238 sheet: -0.06 (0.23), residues: 469 loop : -1.69 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 107 TYR 0.022 0.002 TYR F 324 PHE 0.029 0.002 PHE D 94 TRP 0.034 0.003 TRP A 628 HIS 0.007 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 9227) covalent geometry : angle 0.79699 (12474) hydrogen bonds : bond 0.04505 ( 390) hydrogen bonds : angle 5.54212 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 592 ILE cc_start: 0.8964 (tt) cc_final: 0.8277 (tt) REVERT: A 851 MET cc_start: 0.7732 (ttt) cc_final: 0.7442 (tmm) REVERT: D 109 HIS cc_start: 0.8925 (m-70) cc_final: 0.8715 (m-70) REVERT: D 124 ASP cc_start: 0.9243 (p0) cc_final: 0.9042 (p0) REVERT: D 160 ASP cc_start: 0.8256 (m-30) cc_final: 0.7929 (t0) REVERT: F 317 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8564 (t0) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.0843 time to fit residues: 13.1383 Evaluate side-chains 103 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.113481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075202 restraints weight = 20453.056| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.83 r_work: 0.3087 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9227 Z= 0.121 Angle : 0.673 15.745 12474 Z= 0.341 Chirality : 0.046 0.181 1300 Planarity : 0.004 0.051 1611 Dihedral : 5.376 20.161 1251 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.55 % Allowed : 8.58 % Favored : 89.87 % 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: -0.64 (0.26), residues: 1107 helix: 0.38 (0.34), residues: 238 sheet: 0.12 (0.23), residues: 479 loop : -1.54 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 423 TYR 0.013 0.001 TYR A 815 PHE 0.027 0.001 PHE D 94 TRP 0.032 0.002 TRP A 628 HIS 0.002 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9227) covalent geometry : angle 0.67345 (12474) hydrogen bonds : bond 0.03795 ( 390) hydrogen bonds : angle 5.05816 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6665 (t) REVERT: A 592 ILE cc_start: 0.8872 (tt) cc_final: 0.8492 (tt) REVERT: A 883 GLN cc_start: 0.8824 (pp30) cc_final: 0.8475 (pp30) REVERT: D 124 ASP cc_start: 0.9279 (p0) cc_final: 0.9054 (p0) REVERT: F 74 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8033 (t70) REVERT: F 285 TYR cc_start: 0.8874 (t80) cc_final: 0.8598 (t80) REVERT: F 426 PHE cc_start: 0.8757 (t80) cc_final: 0.8354 (t80) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.0818 time to fit residues: 13.5409 Evaluate side-chains 102 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 311 GLN A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.112973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074392 restraints weight = 20589.122| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.85 r_work: 0.3082 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9227 Z= 0.134 Angle : 0.645 14.184 12474 Z= 0.328 Chirality : 0.045 0.162 1300 Planarity : 0.004 0.053 1611 Dihedral : 5.119 19.766 1251 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.65 % Allowed : 10.96 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1107 helix: 0.51 (0.34), residues: 238 sheet: 0.25 (0.23), residues: 482 loop : -1.45 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 423 TYR 0.014 0.001 TYR A 815 PHE 0.027 0.001 PHE A 314 TRP 0.041 0.002 TRP A 628 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9227) covalent geometry : angle 0.64468 (12474) hydrogen bonds : bond 0.03570 ( 390) hydrogen bonds : angle 4.86526 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7602 (mmm) cc_final: 0.7306 (mmm) REVERT: A 807 MET cc_start: 0.8327 (ptm) cc_final: 0.7756 (ppp) REVERT: A 854 MET cc_start: 0.8060 (mmm) cc_final: 0.7444 (mmm) REVERT: A 883 GLN cc_start: 0.8823 (pp30) cc_final: 0.8506 (pp30) REVERT: D 124 ASP cc_start: 0.9364 (p0) cc_final: 0.9156 (p0) REVERT: D 243 ASN cc_start: 0.9203 (m-40) cc_final: 0.8854 (p0) REVERT: F 74 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8050 (t70) REVERT: F 157 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.8772 (m-70) REVERT: F 409 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8335 (mt-10) REVERT: F 426 PHE cc_start: 0.8826 (t80) cc_final: 0.8363 (t80) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.0832 time to fit residues: 13.3130 Evaluate side-chains 103 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN D 130 GLN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.113317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074490 restraints weight = 20624.306| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.84 r_work: 0.3070 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9227 Z= 0.146 Angle : 0.637 12.830 12474 Z= 0.324 Chirality : 0.045 0.177 1300 Planarity : 0.004 0.051 1611 Dihedral : 5.006 20.104 1251 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.59 % Allowed : 11.69 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.26), residues: 1107 helix: 0.61 (0.34), residues: 238 sheet: 0.21 (0.23), residues: 487 loop : -1.40 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 230 TYR 0.015 0.001 TYR F 285 PHE 0.026 0.001 PHE D 94 TRP 0.040 0.002 TRP A 628 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9227) covalent geometry : angle 0.63719 (12474) hydrogen bonds : bond 0.03472 ( 390) hydrogen bonds : angle 4.79059 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7642 (mmm) cc_final: 0.7332 (mmm) REVERT: A 510 THR cc_start: 0.7022 (OUTLIER) cc_final: 0.6573 (t) REVERT: A 807 MET cc_start: 0.8337 (ptm) cc_final: 0.7841 (ppp) REVERT: A 854 MET cc_start: 0.7885 (mmm) cc_final: 0.7507 (tmm) REVERT: A 883 GLN cc_start: 0.8860 (pp30) cc_final: 0.8533 (pp30) REVERT: D 124 ASP cc_start: 0.9371 (p0) cc_final: 0.9149 (p0) REVERT: D 259 ASN cc_start: 0.9550 (m-40) cc_final: 0.9056 (p0) REVERT: F 74 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8073 (t70) REVERT: F 89 MET cc_start: 0.9150 (ttt) cc_final: 0.8848 (ttt) REVERT: F 157 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8788 (m-70) REVERT: F 285 TYR cc_start: 0.8896 (t80) cc_final: 0.8667 (t80) REVERT: F 426 PHE cc_start: 0.8852 (t80) cc_final: 0.8439 (t80) outliers start: 25 outliers final: 19 residues processed: 115 average time/residue: 0.0723 time to fit residues: 12.2687 Evaluate side-chains 107 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 130 GLN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.074381 restraints weight = 20675.505| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.83 r_work: 0.3068 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9227 Z= 0.152 Angle : 0.635 12.642 12474 Z= 0.325 Chirality : 0.045 0.160 1300 Planarity : 0.004 0.052 1611 Dihedral : 4.955 20.398 1251 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.00 % Allowed : 12.72 % Favored : 84.28 % 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: -0.42 (0.26), residues: 1107 helix: 0.69 (0.35), residues: 236 sheet: 0.17 (0.23), residues: 487 loop : -1.39 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 230 TYR 0.014 0.001 TYR F 285 PHE 0.025 0.001 PHE D 94 TRP 0.046 0.002 TRP A 628 HIS 0.002 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9227) covalent geometry : angle 0.63496 (12474) hydrogen bonds : bond 0.03515 ( 390) hydrogen bonds : angle 4.76576 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7684 (mmm) cc_final: 0.7359 (mmm) REVERT: A 510 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6531 (t) REVERT: A 807 MET cc_start: 0.8389 (ptm) cc_final: 0.7966 (ppp) REVERT: A 851 MET cc_start: 0.7813 (ttt) cc_final: 0.7503 (tmm) REVERT: A 883 GLN cc_start: 0.8836 (pp30) cc_final: 0.8527 (pp30) REVERT: D 124 ASP cc_start: 0.9371 (p0) cc_final: 0.9152 (p0) REVERT: D 236 ASP cc_start: 0.9327 (m-30) cc_final: 0.9118 (p0) REVERT: D 243 ASN cc_start: 0.9218 (m-40) cc_final: 0.8865 (p0) REVERT: D 259 ASN cc_start: 0.9524 (m-40) cc_final: 0.9083 (p0) REVERT: F 74 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (t70) REVERT: F 157 HIS cc_start: 0.9026 (OUTLIER) cc_final: 0.8778 (m-70) REVERT: F 285 TYR cc_start: 0.8905 (t80) cc_final: 0.8693 (t80) REVERT: F 409 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 426 PHE cc_start: 0.8888 (t80) cc_final: 0.8498 (t80) outliers start: 29 outliers final: 20 residues processed: 110 average time/residue: 0.0723 time to fit residues: 12.1378 Evaluate side-chains 108 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 130 GLN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.110672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072603 restraints weight = 20463.634| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.77 r_work: 0.3062 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9227 Z= 0.176 Angle : 0.651 12.413 12474 Z= 0.333 Chirality : 0.045 0.170 1300 Planarity : 0.004 0.051 1611 Dihedral : 4.971 20.603 1251 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.00 % Allowed : 12.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.26), residues: 1107 helix: 0.68 (0.35), residues: 238 sheet: 0.12 (0.23), residues: 487 loop : -1.39 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 230 TYR 0.034 0.001 TYR A 725 PHE 0.024 0.001 PHE D 94 TRP 0.044 0.002 TRP A 628 HIS 0.003 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9227) covalent geometry : angle 0.65127 (12474) hydrogen bonds : bond 0.03469 ( 390) hydrogen bonds : angle 4.76251 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7714 (mmm) cc_final: 0.7384 (mmm) REVERT: A 510 THR cc_start: 0.6886 (OUTLIER) cc_final: 0.6429 (t) REVERT: A 807 MET cc_start: 0.8444 (ptm) cc_final: 0.8146 (ppp) REVERT: A 851 MET cc_start: 0.7807 (ttt) cc_final: 0.7563 (tmm) REVERT: A 883 GLN cc_start: 0.8748 (pp30) cc_final: 0.8406 (pp30) REVERT: D 124 ASP cc_start: 0.9361 (p0) cc_final: 0.9144 (p0) REVERT: D 243 ASN cc_start: 0.9190 (m-40) cc_final: 0.8854 (p0) REVERT: D 259 ASN cc_start: 0.9491 (m-40) cc_final: 0.9065 (p0) REVERT: F 74 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (t70) REVERT: F 426 PHE cc_start: 0.8865 (t80) cc_final: 0.8506 (t80) outliers start: 29 outliers final: 23 residues processed: 107 average time/residue: 0.0729 time to fit residues: 11.8105 Evaluate side-chains 107 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075674 restraints weight = 20588.870| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.83 r_work: 0.3097 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9227 Z= 0.106 Angle : 0.624 11.955 12474 Z= 0.318 Chirality : 0.044 0.172 1300 Planarity : 0.004 0.051 1611 Dihedral : 4.764 20.988 1251 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.96 % Allowed : 13.75 % Favored : 84.28 % 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: -0.36 (0.26), residues: 1107 helix: 0.68 (0.35), residues: 239 sheet: 0.25 (0.24), residues: 488 loop : -1.40 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 423 TYR 0.025 0.001 TYR A 725 PHE 0.024 0.001 PHE D 94 TRP 0.025 0.002 TRP A 628 HIS 0.005 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9227) covalent geometry : angle 0.62382 (12474) hydrogen bonds : bond 0.03251 ( 390) hydrogen bonds : angle 4.64096 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7703 (mmm) cc_final: 0.7378 (mmm) REVERT: A 510 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6497 (t) REVERT: A 807 MET cc_start: 0.8449 (ptm) cc_final: 0.7900 (ppp) REVERT: A 851 MET cc_start: 0.7824 (ttt) cc_final: 0.7548 (tmm) REVERT: A 883 GLN cc_start: 0.8819 (pp30) cc_final: 0.8458 (pp30) REVERT: D 124 ASP cc_start: 0.9350 (p0) cc_final: 0.9115 (p0) REVERT: D 243 ASN cc_start: 0.9235 (m-40) cc_final: 0.8901 (p0) REVERT: D 259 ASN cc_start: 0.9509 (m-40) cc_final: 0.9128 (p0) REVERT: F 74 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8101 (t70) REVERT: F 406 MET cc_start: 0.8734 (mtp) cc_final: 0.8533 (mtt) outliers start: 19 outliers final: 16 residues processed: 105 average time/residue: 0.0732 time to fit residues: 11.6018 Evaluate side-chains 100 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.112020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073431 restraints weight = 20591.970| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.81 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9227 Z= 0.185 Angle : 0.659 12.304 12474 Z= 0.339 Chirality : 0.044 0.158 1300 Planarity : 0.004 0.051 1611 Dihedral : 4.824 20.714 1251 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.28 % Allowed : 14.58 % Favored : 83.14 % 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: -0.44 (0.26), residues: 1107 helix: 0.65 (0.34), residues: 240 sheet: 0.15 (0.24), residues: 487 loop : -1.40 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 232 TYR 0.029 0.001 TYR A 725 PHE 0.023 0.001 PHE D 94 TRP 0.020 0.002 TRP A 628 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9227) covalent geometry : angle 0.65861 (12474) hydrogen bonds : bond 0.03476 ( 390) hydrogen bonds : angle 4.72850 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7728 (mmm) cc_final: 0.7389 (mmm) REVERT: A 510 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6505 (t) REVERT: A 807 MET cc_start: 0.8456 (ptm) cc_final: 0.7893 (ppp) REVERT: A 851 MET cc_start: 0.7838 (ttt) cc_final: 0.7518 (tmm) REVERT: A 854 MET cc_start: 0.7616 (mmm) cc_final: 0.7326 (tmm) REVERT: A 883 GLN cc_start: 0.8820 (pp30) cc_final: 0.8411 (pp30) REVERT: D 124 ASP cc_start: 0.9382 (p0) cc_final: 0.9175 (p0) REVERT: D 259 ASN cc_start: 0.9507 (m-40) cc_final: 0.9130 (p0) REVERT: F 74 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8181 (t70) outliers start: 22 outliers final: 18 residues processed: 102 average time/residue: 0.0713 time to fit residues: 10.7042 Evaluate side-chains 102 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072832 restraints weight = 20844.063| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.84 r_work: 0.3043 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9227 Z= 0.214 Angle : 0.689 13.154 12474 Z= 0.351 Chirality : 0.045 0.176 1300 Planarity : 0.004 0.052 1611 Dihedral : 4.935 21.112 1251 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.48 % Allowed : 14.27 % Favored : 83.25 % 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: -0.56 (0.26), residues: 1107 helix: 0.61 (0.34), residues: 238 sheet: 0.03 (0.24), residues: 489 loop : -1.44 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 32 TYR 0.030 0.001 TYR A 725 PHE 0.023 0.001 PHE D 94 TRP 0.018 0.002 TRP A 628 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9227) covalent geometry : angle 0.68906 (12474) hydrogen bonds : bond 0.03614 ( 390) hydrogen bonds : angle 4.81909 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7798 (mmm) cc_final: 0.7468 (mmm) REVERT: A 510 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6524 (t) REVERT: A 807 MET cc_start: 0.8460 (ptm) cc_final: 0.7836 (ppp) REVERT: A 851 MET cc_start: 0.7830 (ttt) cc_final: 0.7512 (tmm) REVERT: A 854 MET cc_start: 0.7655 (mmm) cc_final: 0.7431 (mmm) REVERT: A 883 GLN cc_start: 0.8867 (pp30) cc_final: 0.8387 (pp30) REVERT: D 72 MET cc_start: 0.7569 (mpp) cc_final: 0.6527 (mtt) REVERT: D 243 ASN cc_start: 0.9284 (m-40) cc_final: 0.8976 (p0) REVERT: D 259 ASN cc_start: 0.9524 (m-40) cc_final: 0.9139 (p0) REVERT: F 74 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8219 (t70) outliers start: 24 outliers final: 19 residues processed: 98 average time/residue: 0.0702 time to fit residues: 10.0813 Evaluate side-chains 101 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.0000 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.111075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073232 restraints weight = 20128.425| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.73 r_work: 0.3074 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9227 Z= 0.138 Angle : 0.660 13.104 12474 Z= 0.336 Chirality : 0.044 0.170 1300 Planarity : 0.004 0.050 1611 Dihedral : 4.821 21.316 1251 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 2.17 % Allowed : 14.58 % Favored : 83.25 % 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: -0.48 (0.26), residues: 1107 helix: 0.65 (0.34), residues: 238 sheet: 0.09 (0.24), residues: 489 loop : -1.40 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 230 TYR 0.026 0.001 TYR A 725 PHE 0.023 0.001 PHE D 94 TRP 0.015 0.001 TRP A 628 HIS 0.006 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9227) covalent geometry : angle 0.66035 (12474) hydrogen bonds : bond 0.03422 ( 390) hydrogen bonds : angle 4.75474 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2681.88 seconds wall clock time: 46 minutes 37.12 seconds (2797.12 seconds total)