Starting phenix.real_space_refine on Tue Mar 3 17:47:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.map" model { file = "/net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjh_51392/03_2026/9gjh_51392.cif" } resolution = 3.0 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= 0.002 sd= 0.148 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 69 5.16 5 C 4684 2.51 5 N 1262 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7521 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5103 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 17, 'TRANS': 627} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.21 Number of scatterers: 7521 At special positions: 0 Unit cell: (89.856, 91.52, 112.32, 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 69 16.00 O 1506 8.00 N 1262 7.00 C 4684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " distance=2.03 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG H 701 " - " ASN H 198 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 271.1 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 22 sheets defined 15.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 118 through 122 removed outlier: 3.502A pdb=" N VAL H 122 " --> pdb=" O TRP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 188 through 197 removed outlier: 3.798A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.727A pdb=" N LEU H 241 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.609A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 565 removed outlier: 4.355A pdb=" N GLU H 565 " --> pdb=" O SER H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.578A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.568A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing sheet with id=AA1, first strand: chain 'H' and resid 106 through 108 removed outlier: 3.839A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 131 through 134 removed outlier: 6.279A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 259 through 262 removed outlier: 3.787A pdb=" N VAL H 260 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR H 214 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR H 248 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 216 " --> pdb=" O THR H 248 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR H 250 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE H 218 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA H 217 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU H 318 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456 removed outlier: 7.503A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA8, first strand: chain 'H' and resid 512 through 514 removed outlier: 6.472A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 543 Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 573 Processing sheet with id=AB2, first strand: chain 'H' and resid 589 through 591 removed outlier: 3.926A pdb=" N CYS H 622 " --> pdb=" O SER H 590 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 601 through 602 removed outlier: 3.699A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 628 through 631 Processing sheet with id=AB5, first strand: chain 'H' and resid 654 through 658 Processing sheet with id=AB6, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.103A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB8, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'L' and resid 103 through 107 Processing sheet with id=AC1, first strand: chain 'L' and resid 157 through 160 Processing sheet with id=AC2, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC3, first strand: chain 'L' and resid 207 through 212 Processing sheet with id=AC4, first strand: chain 'L' and resid 240 through 244 196 hydrogen bonds defined for protein. 492 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: 1.17 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2407 1.34 - 1.46: 1630 1.46 - 1.58: 3555 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 7677 Sorted by residual: bond pdb=" CB CYS H 404 " pdb=" SG CYS H 404 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.27e+00 bond pdb=" CA VAL H 479 " pdb=" CB VAL H 479 " ideal model delta sigma weight residual 1.537 1.550 -0.013 1.29e-02 6.01e+03 1.05e+00 bond pdb=" CB ASP H 334 " pdb=" CG ASP H 334 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 8.90e-01 bond pdb=" CB GLU H 332 " pdb=" CG GLU H 332 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.68e-01 bond pdb=" CG ARG L 251 " pdb=" CD ARG L 251 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.52e-01 ... (remaining 7672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10059 1.18 - 2.36: 250 2.36 - 3.54: 57 3.54 - 4.73: 15 4.73 - 5.91: 8 Bond angle restraints: 10389 Sorted by residual: angle pdb=" N TRP L 223 " pdb=" CA TRP L 223 " pdb=" C TRP L 223 " ideal model delta sigma weight residual 109.81 115.72 -5.91 2.21e+00 2.05e-01 7.15e+00 angle pdb=" N GLY H 593 " pdb=" CA GLY H 593 " pdb=" C GLY H 593 " ideal model delta sigma weight residual 110.87 114.55 -3.68 1.54e+00 4.22e-01 5.71e+00 angle pdb=" CB GLU H 332 " pdb=" CG GLU H 332 " pdb=" CD GLU H 332 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.70e+00 3.46e-01 3.95e+00 angle pdb=" C1 NAG H 701 " pdb=" O5 NAG H 701 " pdb=" C5 NAG H 701 " ideal model delta sigma weight residual 113.21 118.97 -5.76 3.00e+00 1.11e-01 3.69e+00 angle pdb=" CA CYS H 539 " pdb=" CB CYS H 539 " pdb=" SG CYS H 539 " ideal model delta sigma weight residual 114.40 118.54 -4.14 2.30e+00 1.89e-01 3.25e+00 ... (remaining 10384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.29: 4432 24.29 - 48.58: 355 48.58 - 72.87: 58 72.87 - 97.16: 28 97.16 - 121.45: 1 Dihedral angle restraints: 4874 sinusoidal: 2149 harmonic: 2725 Sorted by residual: dihedral pdb=" CB CYS H 477 " pdb=" SG CYS H 477 " pdb=" SG CYS H 515 " pdb=" CB CYS H 515 " ideal model delta sinusoidal sigma weight residual -86.00 -170.25 84.25 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS H 586 " pdb=" SG CYS H 586 " pdb=" SG CYS H 611 " pdb=" CB CYS H 611 " ideal model delta sinusoidal sigma weight residual 93.00 176.61 -83.61 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS H 395 " pdb=" SG CYS H 395 " pdb=" SG CYS H 404 " pdb=" CB CYS H 404 " ideal model delta sinusoidal sigma weight residual -86.00 -158.93 72.93 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 4871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 755 0.035 - 0.070: 293 0.070 - 0.105: 67 0.105 - 0.139: 41 0.139 - 0.174: 4 Chirality restraints: 1160 Sorted by residual: chirality pdb=" C1 NAG H 701 " pdb=" ND2 ASN H 198 " pdb=" C2 NAG H 701 " pdb=" O5 NAG H 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN H 337 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1157 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 479 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO H 480 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 480 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 480 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 231 " -0.005 2.00e-02 2.50e+03 1.18e-02 2.78e+00 pdb=" CG TYR L 231 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR L 231 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 231 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR L 231 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR L 231 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR L 231 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 231 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 364 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO H 365 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " 0.022 5.00e-02 4.00e+02 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 255 2.70 - 3.25: 7230 3.25 - 3.80: 11909 3.80 - 4.35: 15901 4.35 - 4.90: 26981 Nonbonded interactions: 62276 Sorted by model distance: nonbonded pdb=" OG SER H 339 " pdb=" O6 NAG B 1 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP H 172 " pdb=" O6 MAN B 5 " model vdw 2.174 3.040 nonbonded pdb=" NH2 ARG H 394 " pdb=" O ASP H 405 " model vdw 2.180 3.120 nonbonded pdb=" ND2 ASN L 84 " pdb=" OD2 ASP L 95 " model vdw 2.209 3.120 nonbonded pdb=" ND2 ASN H 576 " pdb=" OD1 ASP H 647 " model vdw 2.209 3.120 ... (remaining 62271 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.003 0.037 7714 Z= 0.130 Angle : 0.534 7.673 10474 Z= 0.275 Chirality : 0.043 0.174 1160 Planarity : 0.004 0.042 1325 Dihedral : 17.859 121.454 3048 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.12 % Allowed : 23.49 % Favored : 76.39 % 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: -0.35 (0.28), residues: 914 helix: -0.52 (0.58), residues: 85 sheet: -0.77 (0.37), residues: 185 loop : 0.06 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 251 TYR 0.027 0.001 TYR L 231 PHE 0.008 0.001 PHE H 140 TRP 0.010 0.001 TRP L 223 HIS 0.004 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7677) covalent geometry : angle 0.51375 (10389) SS BOND : bond 0.00190 ( 26) SS BOND : angle 1.47313 ( 52) hydrogen bonds : bond 0.23214 ( 188) hydrogen bonds : angle 9.20540 ( 492) link_ALPHA1-2 : bond 0.00214 ( 2) link_ALPHA1-2 : angle 1.52131 ( 6) link_ALPHA1-3 : bond 0.00609 ( 1) link_ALPHA1-3 : angle 1.59247 ( 3) link_ALPHA1-6 : bond 0.00602 ( 1) link_ALPHA1-6 : angle 1.16659 ( 3) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 1.98458 ( 12) link_NAG-ASN : bond 0.00290 ( 3) link_NAG-ASN : angle 2.54508 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: H 469 ASP cc_start: 0.8192 (p0) cc_final: 0.7733 (p0) REVERT: L 39 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7244 (mptt) REVERT: L 64 GLU cc_start: 0.8172 (pt0) cc_final: 0.7279 (mp0) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.5255 time to fit residues: 44.7517 Evaluate side-chains 73 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 574 ASN L 65 ASN ** L 187 ASN ** 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 = 0.4218 r_free = 0.4218 target = 0.199673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156827 restraints weight = 7750.054| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.46 r_work: 0.3601 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7714 Z= 0.199 Angle : 0.630 9.193 10474 Z= 0.322 Chirality : 0.047 0.204 1160 Planarity : 0.004 0.044 1325 Dihedral : 11.285 107.850 1258 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.34 % Allowed : 20.96 % Favored : 74.70 % 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: -0.52 (0.28), residues: 914 helix: -0.99 (0.54), residues: 91 sheet: -0.67 (0.37), residues: 181 loop : -0.07 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 186 TYR 0.025 0.002 TYR H 27 PHE 0.014 0.002 PHE H 370 TRP 0.012 0.002 TRP H 66 HIS 0.005 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7677) covalent geometry : angle 0.61367 (10389) SS BOND : bond 0.00346 ( 26) SS BOND : angle 1.03024 ( 52) hydrogen bonds : bond 0.04302 ( 188) hydrogen bonds : angle 6.85442 ( 492) link_ALPHA1-2 : bond 0.00327 ( 2) link_ALPHA1-2 : angle 1.76211 ( 6) link_ALPHA1-3 : bond 0.01135 ( 1) link_ALPHA1-3 : angle 1.12913 ( 3) link_ALPHA1-6 : bond 0.00259 ( 1) link_ALPHA1-6 : angle 1.36711 ( 3) link_BETA1-4 : bond 0.00524 ( 4) link_BETA1-4 : angle 2.60516 ( 12) link_NAG-ASN : bond 0.00476 ( 3) link_NAG-ASN : angle 3.02291 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: H 89 VAL cc_start: 0.7604 (p) cc_final: 0.7148 (m) REVERT: H 220 PHE cc_start: 0.7779 (m-80) cc_final: 0.7488 (m-80) REVERT: H 469 ASP cc_start: 0.8096 (p0) cc_final: 0.7722 (p0) REVERT: H 566 MET cc_start: 0.7815 (mtp) cc_final: 0.7567 (mtm) REVERT: L 23 SER cc_start: 0.8489 (m) cc_final: 0.8216 (m) REVERT: L 39 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7105 (mptt) REVERT: L 147 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7213 (mmt) outliers start: 36 outliers final: 14 residues processed: 109 average time/residue: 0.4121 time to fit residues: 48.4041 Evaluate side-chains 92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 381 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN L 65 ASN L 119 ASN L 124 GLN L 187 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.197934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155911 restraints weight = 7807.412| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.24 r_work: 0.3597 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7714 Z= 0.214 Angle : 0.635 9.348 10474 Z= 0.323 Chirality : 0.047 0.198 1160 Planarity : 0.004 0.047 1325 Dihedral : 10.472 107.568 1258 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.42 % Allowed : 21.08 % Favored : 73.49 % 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 (0.28), residues: 914 helix: -1.25 (0.53), residues: 91 sheet: -0.73 (0.37), residues: 180 loop : -0.23 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 186 TYR 0.026 0.002 TYR L 231 PHE 0.016 0.002 PHE H 370 TRP 0.013 0.002 TRP H 66 HIS 0.004 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 7677) covalent geometry : angle 0.61432 (10389) SS BOND : bond 0.00293 ( 26) SS BOND : angle 1.47204 ( 52) hydrogen bonds : bond 0.04213 ( 188) hydrogen bonds : angle 6.54656 ( 492) link_ALPHA1-2 : bond 0.00150 ( 2) link_ALPHA1-2 : angle 1.78402 ( 6) link_ALPHA1-3 : bond 0.00871 ( 1) link_ALPHA1-3 : angle 1.22457 ( 3) link_ALPHA1-6 : bond 0.00246 ( 1) link_ALPHA1-6 : angle 1.37916 ( 3) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 2.40761 ( 12) link_NAG-ASN : bond 0.00416 ( 3) link_NAG-ASN : angle 3.21599 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: H 89 VAL cc_start: 0.7680 (p) cc_final: 0.7277 (m) REVERT: H 220 PHE cc_start: 0.7714 (m-80) cc_final: 0.7268 (m-80) REVERT: H 469 ASP cc_start: 0.8158 (p0) cc_final: 0.7812 (p0) REVERT: H 566 MET cc_start: 0.7883 (mtp) cc_final: 0.7656 (mtm) REVERT: L 23 SER cc_start: 0.8516 (m) cc_final: 0.8247 (m) REVERT: L 39 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7189 (mptt) REVERT: L 58 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.7022 (p) outliers start: 45 outliers final: 19 residues processed: 122 average time/residue: 0.3961 time to fit residues: 52.2375 Evaluate side-chains 99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 381 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 373 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.199333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157551 restraints weight = 7883.082| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.27 r_work: 0.3618 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7714 Z= 0.160 Angle : 0.596 8.606 10474 Z= 0.304 Chirality : 0.046 0.198 1160 Planarity : 0.004 0.046 1325 Dihedral : 9.834 107.058 1258 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.22 % Allowed : 22.53 % Favored : 73.25 % 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: -0.74 (0.28), residues: 914 helix: -1.20 (0.54), residues: 91 sheet: -0.82 (0.37), residues: 180 loop : -0.22 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 553 TYR 0.027 0.001 TYR L 231 PHE 0.014 0.002 PHE H 258 TRP 0.010 0.001 TRP L 223 HIS 0.004 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7677) covalent geometry : angle 0.57719 (10389) SS BOND : bond 0.00279 ( 26) SS BOND : angle 1.27023 ( 52) hydrogen bonds : bond 0.03624 ( 188) hydrogen bonds : angle 6.24200 ( 492) link_ALPHA1-2 : bond 0.00264 ( 2) link_ALPHA1-2 : angle 1.73599 ( 6) link_ALPHA1-3 : bond 0.01051 ( 1) link_ALPHA1-3 : angle 1.28047 ( 3) link_ALPHA1-6 : bond 0.00259 ( 1) link_ALPHA1-6 : angle 1.46142 ( 3) link_BETA1-4 : bond 0.00473 ( 4) link_BETA1-4 : angle 2.22791 ( 12) link_NAG-ASN : bond 0.00261 ( 3) link_NAG-ASN : angle 3.07142 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.8109 (t0) cc_final: 0.7818 (t0) REVERT: H 89 VAL cc_start: 0.7700 (p) cc_final: 0.7309 (m) REVERT: H 107 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: H 220 PHE cc_start: 0.7684 (m-80) cc_final: 0.7144 (m-80) REVERT: H 469 ASP cc_start: 0.8164 (p0) cc_final: 0.7846 (p0) REVERT: H 509 TYR cc_start: 0.8339 (m-80) cc_final: 0.7849 (m-10) REVERT: H 555 LYS cc_start: 0.7828 (mttm) cc_final: 0.7387 (mttp) REVERT: H 566 MET cc_start: 0.7850 (mtp) cc_final: 0.7646 (mtm) REVERT: L 39 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7175 (mptt) REVERT: L 64 GLU cc_start: 0.8336 (pt0) cc_final: 0.7271 (mp0) outliers start: 35 outliers final: 21 residues processed: 111 average time/residue: 0.4284 time to fit residues: 50.8662 Evaluate side-chains 101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 381 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 373 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.197969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156528 restraints weight = 7749.731| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.24 r_work: 0.3593 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7714 Z= 0.191 Angle : 0.616 9.382 10474 Z= 0.313 Chirality : 0.047 0.197 1160 Planarity : 0.004 0.048 1325 Dihedral : 9.653 106.739 1258 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.66 % Allowed : 22.29 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.27), residues: 914 helix: -1.40 (0.51), residues: 97 sheet: -0.88 (0.37), residues: 175 loop : -0.28 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 186 TYR 0.027 0.002 TYR L 231 PHE 0.016 0.002 PHE H 258 TRP 0.013 0.001 TRP H 66 HIS 0.004 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7677) covalent geometry : angle 0.59547 (10389) SS BOND : bond 0.00345 ( 26) SS BOND : angle 1.45733 ( 52) hydrogen bonds : bond 0.03699 ( 188) hydrogen bonds : angle 6.18589 ( 492) link_ALPHA1-2 : bond 0.00197 ( 2) link_ALPHA1-2 : angle 1.74742 ( 6) link_ALPHA1-3 : bond 0.01005 ( 1) link_ALPHA1-3 : angle 1.31383 ( 3) link_ALPHA1-6 : bond 0.00262 ( 1) link_ALPHA1-6 : angle 1.48836 ( 3) link_BETA1-4 : bond 0.00446 ( 4) link_BETA1-4 : angle 2.19822 ( 12) link_NAG-ASN : bond 0.00272 ( 3) link_NAG-ASN : angle 3.09381 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: H 89 VAL cc_start: 0.7842 (p) cc_final: 0.7425 (m) REVERT: H 107 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: H 555 LYS cc_start: 0.7863 (mttm) cc_final: 0.7404 (mttp) REVERT: L 39 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7164 (mptt) REVERT: L 58 VAL cc_start: 0.7213 (OUTLIER) cc_final: 0.6976 (p) outliers start: 47 outliers final: 28 residues processed: 124 average time/residue: 0.4173 time to fit residues: 55.6081 Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 381 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 69 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 373 ASN H 576 ASN H 643 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.201697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160433 restraints weight = 7793.607| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.27 r_work: 0.3621 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7714 Z= 0.123 Angle : 0.579 8.434 10474 Z= 0.294 Chirality : 0.045 0.236 1160 Planarity : 0.004 0.046 1325 Dihedral : 9.055 105.823 1258 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.94 % Allowed : 23.49 % Favored : 71.57 % 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 (0.28), residues: 914 helix: -1.26 (0.52), residues: 97 sheet: -0.82 (0.38), residues: 165 loop : -0.25 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 186 TYR 0.024 0.001 TYR L 231 PHE 0.014 0.002 PHE H 258 TRP 0.011 0.001 TRP L 223 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7677) covalent geometry : angle 0.55909 (10389) SS BOND : bond 0.00432 ( 26) SS BOND : angle 1.44057 ( 52) hydrogen bonds : bond 0.03292 ( 188) hydrogen bonds : angle 5.89704 ( 492) link_ALPHA1-2 : bond 0.00290 ( 2) link_ALPHA1-2 : angle 1.61072 ( 6) link_ALPHA1-3 : bond 0.01330 ( 1) link_ALPHA1-3 : angle 1.43288 ( 3) link_ALPHA1-6 : bond 0.00378 ( 1) link_ALPHA1-6 : angle 1.50634 ( 3) link_BETA1-4 : bond 0.00484 ( 4) link_BETA1-4 : angle 2.01728 ( 12) link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 2.89982 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.8012 (t0) cc_final: 0.7778 (t0) REVERT: H 89 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7386 (m) REVERT: H 293 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5065 (tt) REVERT: H 469 ASP cc_start: 0.8219 (p0) cc_final: 0.7896 (p0) REVERT: H 509 TYR cc_start: 0.8348 (m-80) cc_final: 0.7877 (m-10) REVERT: H 555 LYS cc_start: 0.7842 (mttm) cc_final: 0.7398 (mttp) REVERT: H 566 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7795 (mtp) REVERT: L 39 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7138 (mptt) REVERT: L 58 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6904 (p) REVERT: L 64 GLU cc_start: 0.8292 (pt0) cc_final: 0.7297 (mp0) outliers start: 41 outliers final: 22 residues processed: 121 average time/residue: 0.4201 time to fit residues: 54.6262 Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 373 ASN H 494 GLN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.199292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157756 restraints weight = 7757.370| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.27 r_work: 0.3616 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7714 Z= 0.170 Angle : 0.609 9.718 10474 Z= 0.308 Chirality : 0.047 0.227 1160 Planarity : 0.004 0.048 1325 Dihedral : 9.060 104.883 1258 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.18 % Allowed : 23.61 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 914 helix: -1.30 (0.52), residues: 97 sheet: -0.82 (0.37), residues: 176 loop : -0.24 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 186 TYR 0.035 0.001 TYR L 231 PHE 0.014 0.002 PHE H 370 TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7677) covalent geometry : angle 0.58871 (10389) SS BOND : bond 0.00490 ( 26) SS BOND : angle 1.49817 ( 52) hydrogen bonds : bond 0.03535 ( 188) hydrogen bonds : angle 5.88904 ( 492) link_ALPHA1-2 : bond 0.00259 ( 2) link_ALPHA1-2 : angle 1.70766 ( 6) link_ALPHA1-3 : bond 0.01099 ( 1) link_ALPHA1-3 : angle 1.43924 ( 3) link_ALPHA1-6 : bond 0.00452 ( 1) link_ALPHA1-6 : angle 1.48090 ( 3) link_BETA1-4 : bond 0.00453 ( 4) link_BETA1-4 : angle 2.04476 ( 12) link_NAG-ASN : bond 0.00227 ( 3) link_NAG-ASN : angle 2.99972 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.8111 (t0) cc_final: 0.7827 (t0) REVERT: H 89 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7421 (m) REVERT: H 107 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: H 293 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5025 (tt) REVERT: H 469 ASP cc_start: 0.8167 (p0) cc_final: 0.7859 (p0) REVERT: H 555 LYS cc_start: 0.7831 (mttm) cc_final: 0.7395 (mttp) REVERT: H 566 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7841 (mtp) REVERT: L 39 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7152 (mptt) REVERT: L 58 VAL cc_start: 0.7182 (OUTLIER) cc_final: 0.6959 (p) outliers start: 43 outliers final: 25 residues processed: 117 average time/residue: 0.4335 time to fit residues: 54.2779 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 0.0570 chunk 62 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 373 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.201332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159978 restraints weight = 7818.209| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.26 r_work: 0.3639 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7714 Z= 0.134 Angle : 0.598 11.384 10474 Z= 0.303 Chirality : 0.046 0.221 1160 Planarity : 0.004 0.046 1325 Dihedral : 8.700 104.749 1258 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.46 % Allowed : 24.34 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.28), residues: 914 helix: -1.20 (0.52), residues: 97 sheet: -0.77 (0.38), residues: 176 loop : -0.19 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 186 TYR 0.033 0.001 TYR L 231 PHE 0.016 0.002 PHE H 258 TRP 0.012 0.001 TRP L 223 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7677) covalent geometry : angle 0.57783 (10389) SS BOND : bond 0.00359 ( 26) SS BOND : angle 1.48087 ( 52) hydrogen bonds : bond 0.03318 ( 188) hydrogen bonds : angle 5.75587 ( 492) link_ALPHA1-2 : bond 0.00336 ( 2) link_ALPHA1-2 : angle 1.71454 ( 6) link_ALPHA1-3 : bond 0.01342 ( 1) link_ALPHA1-3 : angle 1.24685 ( 3) link_ALPHA1-6 : bond 0.00555 ( 1) link_ALPHA1-6 : angle 1.32722 ( 3) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 2.15371 ( 12) link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 2.93352 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.7988 (t0) cc_final: 0.7772 (t0) REVERT: H 89 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7429 (m) REVERT: H 107 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: H 138 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8066 (t) REVERT: H 172 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7457 (t70) REVERT: H 469 ASP cc_start: 0.8199 (p0) cc_final: 0.7889 (p0) REVERT: H 509 TYR cc_start: 0.8398 (m-80) cc_final: 0.7914 (m-10) REVERT: H 555 LYS cc_start: 0.7852 (mttm) cc_final: 0.7405 (mttp) REVERT: H 566 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7886 (mtp) REVERT: L 39 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7157 (mptt) REVERT: L 58 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6927 (p) outliers start: 37 outliers final: 25 residues processed: 115 average time/residue: 0.4399 time to fit residues: 54.1952 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 258 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 373 ASN H 408 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.200022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158706 restraints weight = 7795.070| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.25 r_work: 0.3620 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7714 Z= 0.153 Angle : 0.611 12.543 10474 Z= 0.308 Chirality : 0.046 0.229 1160 Planarity : 0.004 0.047 1325 Dihedral : 8.631 104.055 1258 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.46 % Allowed : 23.73 % Favored : 71.81 % 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: -0.75 (0.28), residues: 914 helix: -1.24 (0.52), residues: 97 sheet: -0.77 (0.38), residues: 176 loop : -0.23 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 186 TYR 0.036 0.001 TYR L 231 PHE 0.016 0.002 PHE H 258 TRP 0.011 0.001 TRP L 223 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7677) covalent geometry : angle 0.59279 (10389) SS BOND : bond 0.00397 ( 26) SS BOND : angle 1.39109 ( 52) hydrogen bonds : bond 0.03399 ( 188) hydrogen bonds : angle 5.74866 ( 492) link_ALPHA1-2 : bond 0.00292 ( 2) link_ALPHA1-2 : angle 1.67779 ( 6) link_ALPHA1-3 : bond 0.01194 ( 1) link_ALPHA1-3 : angle 1.38134 ( 3) link_ALPHA1-6 : bond 0.00548 ( 1) link_ALPHA1-6 : angle 1.49222 ( 3) link_BETA1-4 : bond 0.00521 ( 4) link_BETA1-4 : angle 2.10809 ( 12) link_NAG-ASN : bond 0.00266 ( 3) link_NAG-ASN : angle 2.94527 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.8063 (t0) cc_final: 0.7809 (t0) REVERT: H 89 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7421 (m) REVERT: H 107 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: H 138 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8059 (t) REVERT: H 172 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7435 (t70) REVERT: H 469 ASP cc_start: 0.8194 (p0) cc_final: 0.7894 (p0) REVERT: H 509 TYR cc_start: 0.8379 (m-80) cc_final: 0.7986 (m-10) REVERT: H 555 LYS cc_start: 0.7842 (mttm) cc_final: 0.7394 (mttp) REVERT: H 566 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: L 39 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7166 (mptt) REVERT: L 58 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6940 (p) REVERT: L 199 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6843 (pp20) outliers start: 37 outliers final: 25 residues processed: 119 average time/residue: 0.4576 time to fit residues: 58.2773 Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 585 SER Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.201146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.160048 restraints weight = 7760.242| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.21 r_work: 0.3642 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7714 Z= 0.135 Angle : 0.606 12.275 10474 Z= 0.307 Chirality : 0.046 0.209 1160 Planarity : 0.004 0.045 1325 Dihedral : 8.449 103.789 1258 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.22 % Allowed : 24.34 % Favored : 71.45 % 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: -0.72 (0.28), residues: 914 helix: -1.19 (0.52), residues: 97 sheet: -0.75 (0.38), residues: 176 loop : -0.22 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 186 TYR 0.033 0.001 TYR L 231 PHE 0.016 0.002 PHE H 258 TRP 0.012 0.001 TRP L 223 HIS 0.003 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7677) covalent geometry : angle 0.58428 (10389) SS BOND : bond 0.00380 ( 26) SS BOND : angle 1.67354 ( 52) hydrogen bonds : bond 0.03236 ( 188) hydrogen bonds : angle 5.68497 ( 492) link_ALPHA1-2 : bond 0.00355 ( 2) link_ALPHA1-2 : angle 1.64622 ( 6) link_ALPHA1-3 : bond 0.01269 ( 1) link_ALPHA1-3 : angle 1.45308 ( 3) link_ALPHA1-6 : bond 0.00595 ( 1) link_ALPHA1-6 : angle 1.47228 ( 3) link_BETA1-4 : bond 0.00543 ( 4) link_BETA1-4 : angle 1.97033 ( 12) link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 2.88323 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: H 51 ASP cc_start: 0.7988 (t0) cc_final: 0.7764 (t0) REVERT: H 89 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7412 (m) REVERT: H 107 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: H 138 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8048 (t) REVERT: H 172 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7385 (t70) REVERT: H 469 ASP cc_start: 0.8183 (p0) cc_final: 0.7886 (p0) REVERT: H 509 TYR cc_start: 0.8372 (m-80) cc_final: 0.7946 (m-10) REVERT: H 555 LYS cc_start: 0.7820 (mttm) cc_final: 0.7364 (mttp) REVERT: L 39 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7139 (mptt) REVERT: L 58 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6889 (p) REVERT: L 199 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6785 (pp20) outliers start: 35 outliers final: 24 residues processed: 114 average time/residue: 0.4334 time to fit residues: 52.8612 Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 258 PHE Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 375 GLU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 522 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 649 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN H 234 ASN L 65 ASN L 119 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160175 restraints weight = 7682.997| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.31 r_work: 0.3657 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7714 Z= 0.133 Angle : 0.599 11.872 10474 Z= 0.303 Chirality : 0.046 0.207 1160 Planarity : 0.004 0.045 1325 Dihedral : 8.273 103.081 1258 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.10 % Allowed : 24.58 % Favored : 71.33 % 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: -0.71 (0.28), residues: 914 helix: -1.17 (0.52), residues: 97 sheet: -0.74 (0.38), residues: 176 loop : -0.22 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 186 TYR 0.032 0.001 TYR L 231 PHE 0.021 0.002 PHE L 37 TRP 0.011 0.001 TRP L 223 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7677) covalent geometry : angle 0.57839 (10389) SS BOND : bond 0.00372 ( 26) SS BOND : angle 1.62692 ( 52) hydrogen bonds : bond 0.03219 ( 188) hydrogen bonds : angle 5.63180 ( 492) link_ALPHA1-2 : bond 0.00325 ( 2) link_ALPHA1-2 : angle 1.61909 ( 6) link_ALPHA1-3 : bond 0.01257 ( 1) link_ALPHA1-3 : angle 1.50611 ( 3) link_ALPHA1-6 : bond 0.00655 ( 1) link_ALPHA1-6 : angle 1.42744 ( 3) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 1.91203 ( 12) link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 2.83806 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.73 seconds wall clock time: 44 minutes 36.02 seconds (2676.02 seconds total)