Starting phenix.real_space_refine on Sun Jul 27 12:13:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.map" model { file = "/net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cui_27000/07_2025/8cui_27000.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.102 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 63 5.16 5 C 6132 2.51 5 N 1491 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9357 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3119 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 11, 'TRANS': 398} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 5.96, per 1000 atoms: 0.64 Number of scatterers: 9357 At special positions: 0 Unit cell: (108.204, 103.944, 75.828, 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 63 16.00 O 1671 8.00 N 1491 7.00 C 6132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 441 " distance=2.95 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 441 " distance=2.95 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 441 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 84.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.678A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.790A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.679A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.547A pdb=" N MET B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.743A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.790A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 4.125A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.967A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.165A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.677A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.624A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.553A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.598A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.546A pdb=" N MET C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.744A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.772A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.790A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.860A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 4.126A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.966A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 429 through 436 removed outlier: 4.164A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.942A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.778A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 732 hydrogen bonds defined for protein. 2160 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: 2.53 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2925 1.34 - 1.46: 1778 1.46 - 1.58: 4675 1.58 - 1.70: 0 1.70 - 1.81: 117 Bond restraints: 9495 Sorted by residual: bond pdb=" N CYS B 269 " pdb=" CA CYS B 269 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N CYS B 441 " pdb=" CA CYS B 441 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.32e+00 bond pdb=" N CYS A 269 " pdb=" CA CYS A 269 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.95e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.90e+00 ... (remaining 9490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 12679 1.71 - 3.42: 173 3.42 - 5.13: 30 5.13 - 6.84: 3 6.84 - 8.55: 3 Bond angle restraints: 12888 Sorted by residual: angle pdb=" CA CYS A 441 " pdb=" C CYS A 441 " pdb=" O CYS A 441 " ideal model delta sigma weight residual 120.90 118.22 2.68 1.07e+00 8.73e-01 6.27e+00 angle pdb=" CA CYS B 441 " pdb=" C CYS B 441 " pdb=" O CYS B 441 " ideal model delta sigma weight residual 120.82 118.20 2.62 1.05e+00 9.07e-01 6.23e+00 angle pdb=" CA CYS C 441 " pdb=" C CYS C 441 " pdb=" O CYS C 441 " ideal model delta sigma weight residual 120.90 118.25 2.65 1.07e+00 8.73e-01 6.13e+00 angle pdb=" CA LEU B 416 " pdb=" CB LEU B 416 " pdb=" CG LEU B 416 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CA LEU C 416 " pdb=" CB LEU C 416 " pdb=" CG LEU C 416 " ideal model delta sigma weight residual 116.30 124.82 -8.52 3.50e+00 8.16e-02 5.93e+00 ... (remaining 12883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5028 17.90 - 35.79: 480 35.79 - 53.69: 147 53.69 - 71.58: 21 71.58 - 89.48: 9 Dihedral angle restraints: 5685 sinusoidal: 2160 harmonic: 3525 Sorted by residual: dihedral pdb=" CB CYS B 269 " pdb=" SG CYS B 269 " pdb=" SG CYS B 441 " pdb=" CB CYS B 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.09 -68.91 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 269 " pdb=" SG CYS C 269 " pdb=" SG CYS C 441 " pdb=" CB CYS C 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.11 -68.89 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS A 269 " pdb=" SG CYS A 269 " pdb=" SG CYS A 441 " pdb=" CB CYS A 441 " ideal model delta sinusoidal sigma weight residual -86.00 -17.12 -68.88 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 5682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1164 0.034 - 0.069: 355 0.069 - 0.103: 90 0.103 - 0.137: 22 0.137 - 0.172: 4 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 441 " pdb=" N CYS B 441 " pdb=" C CYS B 441 " pdb=" CB CYS B 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA CYS A 441 " pdb=" N CYS A 441 " pdb=" C CYS A 441 " pdb=" CB CYS A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 441 " pdb=" N CYS C 441 " pdb=" C CYS C 441 " pdb=" CB CYS C 441 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1632 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ILE C 295 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ILE A 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ILE B 295 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2140 2.79 - 3.32: 9133 3.32 - 3.85: 15322 3.85 - 4.37: 17103 4.37 - 4.90: 31050 Nonbonded interactions: 74748 Sorted by model distance: nonbonded pdb=" O GLY B 392 " pdb=" OG1 THR B 396 " model vdw 2.264 3.040 nonbonded pdb=" O GLY A 392 " pdb=" OG1 THR A 396 " model vdw 2.265 3.040 nonbonded pdb=" O GLY C 392 " pdb=" OG1 THR C 396 " model vdw 2.265 3.040 nonbonded pdb=" O VAL C 20 " pdb=" OG1 THR C 24 " model vdw 2.316 3.040 nonbonded pdb=" O VAL B 20 " pdb=" OG1 THR B 24 " model vdw 2.316 3.040 ... (remaining 74743 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.800 Find NCS groups from input model: 0.160 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.017 0.923 9498 Z= 0.834 Angle : 0.895 43.044 12894 Z= 0.455 Chirality : 0.037 0.172 1635 Planarity : 0.004 0.030 1572 Dihedral : 15.717 89.480 3402 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 22.87 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1212 helix: 1.71 (0.16), residues: 978 sheet: 0.95 (0.68), residues: 54 loop : -1.99 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.11764 ( 732) hydrogen bonds : angle 5.19579 ( 2160) SS BOND : bond 0.92318 ( 3) SS BOND : angle 33.31220 ( 6) covalent geometry : bond 0.00268 ( 9495) covalent geometry : angle 0.53377 (12888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.082 Fit side-chains REVERT: A 252 GLN cc_start: 0.7831 (tt0) cc_final: 0.7048 (tp-100) REVERT: B 37 LEU cc_start: 0.7938 (tp) cc_final: 0.7658 (mp) REVERT: B 165 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7669 (ptpt) REVERT: B 200 TYR cc_start: 0.7839 (m-80) cc_final: 0.7567 (m-80) REVERT: B 205 MET cc_start: 0.8755 (ptm) cc_final: 0.8494 (ptp) REVERT: B 252 GLN cc_start: 0.7788 (tt0) cc_final: 0.7023 (tp-100) REVERT: C 252 GLN cc_start: 0.7726 (tt0) cc_final: 0.6925 (tp-100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 1.3119 time to fit residues: 191.9892 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 111 optimal weight: 3.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113867 restraints weight = 9755.837| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.88 r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9498 Z= 0.119 Angle : 0.483 7.673 12894 Z= 0.257 Chirality : 0.037 0.131 1635 Planarity : 0.004 0.031 1572 Dihedral : 3.564 13.664 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.54 % Allowed : 20.82 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1212 helix: 1.93 (0.16), residues: 990 sheet: 0.65 (0.65), residues: 54 loop : -2.56 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE C 239 TYR 0.007 0.001 TYR C 162 ARG 0.005 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 732) hydrogen bonds : angle 4.18031 ( 2160) SS BOND : bond 0.00844 ( 3) SS BOND : angle 1.91414 ( 6) covalent geometry : bond 0.00213 ( 9495) covalent geometry : angle 0.48144 (12888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7987 (tt0) cc_final: 0.7061 (tp-100) REVERT: A 437 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7482 (tt) REVERT: B 37 LEU cc_start: 0.7621 (tp) cc_final: 0.7356 (mp) REVERT: B 200 TYR cc_start: 0.7799 (m-80) cc_final: 0.7562 (m-80) REVERT: B 205 MET cc_start: 0.8975 (ptm) cc_final: 0.8726 (ptp) REVERT: B 248 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: B 252 GLN cc_start: 0.8044 (tt0) cc_final: 0.7066 (tp-100) REVERT: B 419 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6790 (ttt) REVERT: C 252 GLN cc_start: 0.7929 (tt0) cc_final: 0.6983 (tp-100) REVERT: C 473 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (mtp) outliers start: 26 outliers final: 7 residues processed: 145 average time/residue: 1.1477 time to fit residues: 178.8606 Evaluate side-chains 139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110994 restraints weight = 9825.792| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.89 r_work: 0.3109 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9498 Z= 0.128 Angle : 0.496 8.313 12894 Z= 0.264 Chirality : 0.037 0.177 1635 Planarity : 0.004 0.032 1572 Dihedral : 3.570 14.680 1290 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.74 % Allowed : 19.84 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.24), residues: 1212 helix: 1.91 (0.16), residues: 993 sheet: 0.32 (0.63), residues: 54 loop : -2.48 (0.37), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.007 0.001 TYR A 98 ARG 0.003 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05314 ( 732) hydrogen bonds : angle 4.16740 ( 2160) SS BOND : bond 0.01061 ( 3) SS BOND : angle 0.56945 ( 6) covalent geometry : bond 0.00247 ( 9495) covalent geometry : angle 0.49624 (12888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.8031 (tt0) cc_final: 0.7092 (tp-100) REVERT: B 37 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7304 (mp) REVERT: B 200 TYR cc_start: 0.7820 (m-80) cc_final: 0.7603 (m-80) REVERT: B 205 MET cc_start: 0.9032 (ptm) cc_final: 0.8787 (ptp) REVERT: B 248 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7442 (mpp) REVERT: B 252 GLN cc_start: 0.8069 (tt0) cc_final: 0.7081 (tp-100) REVERT: B 329 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6702 (mpp) REVERT: B 419 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6823 (ttt) REVERT: C 85 ASN cc_start: 0.8114 (p0) cc_final: 0.7911 (p0) REVERT: C 473 MET cc_start: 0.8387 (mtt) cc_final: 0.8079 (mtp) outliers start: 28 outliers final: 11 residues processed: 143 average time/residue: 1.1796 time to fit residues: 180.7383 Evaluate side-chains 147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109643 restraints weight = 9804.161| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.90 r_work: 0.3091 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9498 Z= 0.134 Angle : 0.520 8.132 12894 Z= 0.271 Chirality : 0.038 0.180 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.609 14.790 1290 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.54 % Allowed : 19.75 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.24), residues: 1212 helix: 1.93 (0.16), residues: 975 sheet: 0.12 (0.62), residues: 54 loop : -2.01 (0.39), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.013 0.001 PHE A 240 TYR 0.008 0.001 TYR A 98 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 732) hydrogen bonds : angle 4.17707 ( 2160) SS BOND : bond 0.00860 ( 3) SS BOND : angle 0.43315 ( 6) covalent geometry : bond 0.00265 ( 9495) covalent geometry : angle 0.51965 (12888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7205 (mt-10) REVERT: A 437 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7600 (tt) REVERT: B 37 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7304 (mp) REVERT: B 205 MET cc_start: 0.9028 (ptm) cc_final: 0.8766 (ptp) REVERT: B 248 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: B 252 GLN cc_start: 0.8065 (tt0) cc_final: 0.7050 (tp-100) REVERT: B 329 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6667 (mpp) REVERT: B 419 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6780 (ttt) REVERT: C 473 MET cc_start: 0.8389 (mtt) cc_final: 0.8137 (mtp) outliers start: 26 outliers final: 13 residues processed: 142 average time/residue: 1.1532 time to fit residues: 175.7148 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109355 restraints weight = 9769.383| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.89 r_work: 0.3086 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9498 Z= 0.135 Angle : 0.512 7.855 12894 Z= 0.270 Chirality : 0.038 0.178 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.628 14.773 1290 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.93 % Allowed : 20.43 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1212 helix: 1.89 (0.16), residues: 975 sheet: -0.02 (0.60), residues: 54 loop : -2.11 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.013 0.001 PHE A 240 TYR 0.008 0.001 TYR A 98 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 732) hydrogen bonds : angle 4.18057 ( 2160) SS BOND : bond 0.00882 ( 3) SS BOND : angle 0.46211 ( 6) covalent geometry : bond 0.00269 ( 9495) covalent geometry : angle 0.51252 (12888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 322 GLN cc_start: 0.7841 (tt0) cc_final: 0.6971 (mt0) REVERT: A 437 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7647 (tt) REVERT: B 205 MET cc_start: 0.9032 (ptm) cc_final: 0.8772 (ptp) REVERT: B 248 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: B 252 GLN cc_start: 0.8075 (tt0) cc_final: 0.7059 (tp-100) REVERT: B 318 MET cc_start: 0.7776 (mtm) cc_final: 0.7464 (ttm) REVERT: B 322 GLN cc_start: 0.7709 (tt0) cc_final: 0.6690 (mt0) REVERT: B 406 ILE cc_start: 0.8360 (tt) cc_final: 0.8004 (tp) REVERT: B 419 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6891 (ttt) REVERT: C 252 GLN cc_start: 0.7999 (tt0) cc_final: 0.7020 (tp-100) REVERT: C 322 GLN cc_start: 0.7669 (tt0) cc_final: 0.6653 (mp10) REVERT: C 473 MET cc_start: 0.8370 (mtt) cc_final: 0.8156 (mtp) outliers start: 30 outliers final: 13 residues processed: 148 average time/residue: 1.1573 time to fit residues: 183.7893 Evaluate side-chains 151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 chunk 99 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111999 restraints weight = 9823.848| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.89 r_work: 0.3126 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9498 Z= 0.121 Angle : 0.484 8.215 12894 Z= 0.256 Chirality : 0.037 0.183 1635 Planarity : 0.003 0.032 1572 Dihedral : 3.540 13.275 1290 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.54 % Allowed : 20.92 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1212 helix: 1.94 (0.16), residues: 981 sheet: 0.03 (0.61), residues: 54 loop : -2.57 (0.35), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.007 0.001 TYR C 98 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 732) hydrogen bonds : angle 4.08134 ( 2160) SS BOND : bond 0.00770 ( 3) SS BOND : angle 0.50352 ( 6) covalent geometry : bond 0.00228 ( 9495) covalent geometry : angle 0.48413 (12888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7998 (tt0) cc_final: 0.7062 (tp-100) REVERT: A 318 MET cc_start: 0.7730 (mtm) cc_final: 0.7491 (ttm) REVERT: A 437 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 205 MET cc_start: 0.9037 (ptm) cc_final: 0.8781 (ptp) REVERT: B 248 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: B 252 GLN cc_start: 0.8045 (tt0) cc_final: 0.7064 (tp-100) REVERT: B 318 MET cc_start: 0.7697 (mtm) cc_final: 0.7373 (ttm) REVERT: B 322 GLN cc_start: 0.7649 (tt0) cc_final: 0.6640 (mt0) REVERT: B 406 ILE cc_start: 0.8346 (tt) cc_final: 0.7999 (tp) REVERT: B 419 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6910 (ttt) REVERT: C 252 GLN cc_start: 0.7913 (tt0) cc_final: 0.6967 (tp-100) REVERT: C 322 GLN cc_start: 0.7650 (tt0) cc_final: 0.6630 (mp10) REVERT: C 473 MET cc_start: 0.8320 (mtt) cc_final: 0.8094 (mtp) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 1.1977 time to fit residues: 190.4859 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105737 restraints weight = 9765.581| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.88 r_work: 0.3034 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9498 Z= 0.175 Angle : 0.577 8.389 12894 Z= 0.307 Chirality : 0.041 0.201 1635 Planarity : 0.004 0.035 1572 Dihedral : 3.788 13.980 1290 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.64 % Allowed : 20.92 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1212 helix: 1.65 (0.16), residues: 978 sheet: -0.20 (0.58), residues: 54 loop : -2.27 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 PHE 0.018 0.002 PHE A 240 TYR 0.011 0.002 TYR A 98 ARG 0.002 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.06887 ( 732) hydrogen bonds : angle 4.37680 ( 2160) SS BOND : bond 0.01002 ( 3) SS BOND : angle 1.00874 ( 6) covalent geometry : bond 0.00389 ( 9495) covalent geometry : angle 0.57683 (12888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7871 (mtm) cc_final: 0.7660 (ttm) REVERT: A 419 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6870 (ttt) REVERT: A 437 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7782 (tt) REVERT: B 205 MET cc_start: 0.9037 (ptm) cc_final: 0.8782 (ptp) REVERT: B 248 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: B 252 GLN cc_start: 0.8192 (tt0) cc_final: 0.7174 (tp-100) REVERT: B 318 MET cc_start: 0.7809 (mtm) cc_final: 0.7472 (ttm) REVERT: B 322 GLN cc_start: 0.7805 (tt0) cc_final: 0.6793 (mt0) REVERT: B 406 ILE cc_start: 0.8401 (tt) cc_final: 0.8045 (tp) REVERT: C 322 GLN cc_start: 0.7829 (tt0) cc_final: 0.6815 (mp10) REVERT: C 419 MET cc_start: 0.6896 (ttt) cc_final: 0.6606 (ttt) REVERT: C 473 MET cc_start: 0.8495 (mtt) cc_final: 0.8242 (mtp) outliers start: 27 outliers final: 13 residues processed: 142 average time/residue: 1.2130 time to fit residues: 184.3492 Evaluate side-chains 148 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109636 restraints weight = 9861.457| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.90 r_work: 0.3089 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9498 Z= 0.131 Angle : 0.511 8.319 12894 Z= 0.271 Chirality : 0.038 0.193 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.664 13.507 1290 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.76 % Allowed : 21.70 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1212 helix: 1.97 (0.16), residues: 951 sheet: -0.19 (0.60), residues: 54 loop : -1.55 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE A 240 TYR 0.008 0.001 TYR C 98 ARG 0.004 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 732) hydrogen bonds : angle 4.20344 ( 2160) SS BOND : bond 0.00918 ( 3) SS BOND : angle 0.90169 ( 6) covalent geometry : bond 0.00257 ( 9495) covalent geometry : angle 0.51075 (12888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 252 GLN cc_start: 0.8050 (tt0) cc_final: 0.7113 (tp-100) REVERT: A 318 MET cc_start: 0.7768 (mtm) cc_final: 0.7543 (ttm) REVERT: A 419 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6892 (ttt) REVERT: A 437 ILE cc_start: 0.7921 (tt) cc_final: 0.7701 (tt) REVERT: B 205 MET cc_start: 0.9028 (ptm) cc_final: 0.8767 (ptp) REVERT: B 248 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: B 252 GLN cc_start: 0.8080 (tt0) cc_final: 0.7045 (tp-100) REVERT: B 318 MET cc_start: 0.7708 (mtm) cc_final: 0.7394 (ttm) REVERT: B 320 MET cc_start: 0.8489 (mmm) cc_final: 0.8238 (mmm) REVERT: B 322 GLN cc_start: 0.7716 (tt0) cc_final: 0.6698 (mt0) REVERT: B 406 ILE cc_start: 0.8386 (tt) cc_final: 0.8039 (tp) REVERT: C 252 GLN cc_start: 0.7988 (tt0) cc_final: 0.7015 (tp-100) REVERT: C 322 GLN cc_start: 0.7716 (tt0) cc_final: 0.6713 (mp10) REVERT: C 419 MET cc_start: 0.6879 (ttt) cc_final: 0.6648 (ttt) REVERT: C 473 MET cc_start: 0.8384 (mtt) cc_final: 0.8160 (mtp) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 1.2207 time to fit residues: 183.0529 Evaluate side-chains 146 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110727 restraints weight = 9737.925| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.88 r_work: 0.3107 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9498 Z= 0.128 Angle : 0.508 8.819 12894 Z= 0.269 Chirality : 0.038 0.188 1635 Planarity : 0.004 0.033 1572 Dihedral : 3.592 13.387 1290 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.86 % Allowed : 21.99 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.24), residues: 1212 helix: 1.91 (0.16), residues: 969 sheet: -0.13 (0.61), residues: 54 loop : -1.96 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 PHE 0.011 0.001 PHE B 99 TYR 0.008 0.001 TYR C 98 ARG 0.007 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 732) hydrogen bonds : angle 4.16133 ( 2160) SS BOND : bond 0.00853 ( 3) SS BOND : angle 1.03411 ( 6) covalent geometry : bond 0.00250 ( 9495) covalent geometry : angle 0.50797 (12888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7729 (mtm) cc_final: 0.7505 (ttm) REVERT: A 396 THR cc_start: 0.7858 (p) cc_final: 0.7657 (t) REVERT: A 419 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6754 (ttt) REVERT: A 437 ILE cc_start: 0.7983 (tt) cc_final: 0.7762 (tt) REVERT: B 205 MET cc_start: 0.9026 (ptm) cc_final: 0.8767 (ptp) REVERT: B 248 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7472 (mpp) REVERT: B 252 GLN cc_start: 0.8074 (tt0) cc_final: 0.7075 (tp-100) REVERT: B 318 MET cc_start: 0.7693 (mtm) cc_final: 0.7388 (ttm) REVERT: B 322 GLN cc_start: 0.7696 (tt0) cc_final: 0.6689 (mt0) REVERT: B 406 ILE cc_start: 0.8354 (tt) cc_final: 0.8023 (tp) REVERT: B 419 MET cc_start: 0.6849 (ttt) cc_final: 0.6626 (ttt) REVERT: C 252 GLN cc_start: 0.7982 (tt0) cc_final: 0.7008 (tp-100) REVERT: C 322 GLN cc_start: 0.7692 (tt0) cc_final: 0.6679 (mp10) REVERT: C 406 ILE cc_start: 0.8269 (tt) cc_final: 0.7840 (tp) REVERT: C 419 MET cc_start: 0.6886 (ttt) cc_final: 0.6531 (ttt) outliers start: 19 outliers final: 13 residues processed: 145 average time/residue: 1.1866 time to fit residues: 184.3619 Evaluate side-chains 151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108346 restraints weight = 9856.621| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.89 r_work: 0.3070 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9498 Z= 0.147 Angle : 0.544 8.763 12894 Z= 0.289 Chirality : 0.039 0.196 1635 Planarity : 0.004 0.034 1572 Dihedral : 3.681 13.905 1290 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.66 % Allowed : 22.19 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1212 helix: 1.90 (0.16), residues: 951 sheet: -0.22 (0.60), residues: 54 loop : -1.56 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 19 HIS 0.001 0.000 HIS B 296 PHE 0.014 0.002 PHE A 240 TYR 0.009 0.001 TYR A 98 ARG 0.007 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 732) hydrogen bonds : angle 4.26440 ( 2160) SS BOND : bond 0.00972 ( 3) SS BOND : angle 1.39690 ( 6) covalent geometry : bond 0.00306 ( 9495) covalent geometry : angle 0.54307 (12888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7790 (mtm) cc_final: 0.7562 (ttm) REVERT: A 322 GLN cc_start: 0.7914 (mt0) cc_final: 0.7078 (mt0) REVERT: A 406 ILE cc_start: 0.8325 (tt) cc_final: 0.8052 (tp) REVERT: A 419 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6727 (ttt) REVERT: A 437 ILE cc_start: 0.7997 (tt) cc_final: 0.7777 (tt) REVERT: B 205 MET cc_start: 0.9017 (ptm) cc_final: 0.8756 (ptp) REVERT: B 248 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7525 (mpp) REVERT: B 252 GLN cc_start: 0.8160 (tt0) cc_final: 0.7160 (tp-100) REVERT: B 318 MET cc_start: 0.7789 (mtm) cc_final: 0.7472 (ttm) REVERT: B 322 GLN cc_start: 0.7716 (tt0) cc_final: 0.6693 (mt0) REVERT: B 406 ILE cc_start: 0.8371 (tt) cc_final: 0.8036 (tp) REVERT: B 419 MET cc_start: 0.6796 (ttt) cc_final: 0.6579 (ttt) REVERT: C 322 GLN cc_start: 0.7759 (tt0) cc_final: 0.6752 (mp10) REVERT: C 406 ILE cc_start: 0.8347 (tt) cc_final: 0.7913 (tp) REVERT: C 419 MET cc_start: 0.6842 (ttt) cc_final: 0.6509 (ttt) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 1.1907 time to fit residues: 184.8819 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN C 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104080 restraints weight = 9785.258| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.89 r_work: 0.3009 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9498 Z= 0.209 Angle : 0.635 8.621 12894 Z= 0.338 Chirality : 0.043 0.199 1635 Planarity : 0.005 0.040 1572 Dihedral : 3.977 14.972 1290 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.76 % Allowed : 22.29 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1212 helix: 1.60 (0.16), residues: 948 sheet: 0.52 (0.51), residues: 48 loop : -2.18 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 256 HIS 0.003 0.001 HIS B 296 PHE 0.021 0.002 PHE A 240 TYR 0.012 0.002 TYR A 98 ARG 0.007 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.07648 ( 732) hydrogen bonds : angle 4.49883 ( 2160) SS BOND : bond 0.01172 ( 3) SS BOND : angle 1.92324 ( 6) covalent geometry : bond 0.00488 ( 9495) covalent geometry : angle 0.63344 (12888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7991.70 seconds wall clock time: 137 minutes 2.62 seconds (8222.62 seconds total)